{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and experiment.library_selection = \"PolyA\"", "rows": [[0, "DRR314108", "DRX303511", "DRS233566", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of wild type sibling sample3", "SAMD00399013", null, "sample name:rna rw337 48hpf WT rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399013", "DRX303511", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399013", null, null, null, 23076492885.0, 76679376.0, "DRR314108", "0:150.51 1:150.44", "A:6146969533;C:5373690527;G:5458576301;T:6095818756;N:1437768", 150, 150, null, null, 6146969533, 5373690527, 5458576301, 6095818756, 1437768, "DRX303511", "DRS233566", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.94223, 0.94614, 0.10721, 0.10288, 0.68745, 0.68621, 0.4728, 0.47157, 151, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [1, "DRR314107", "DRX303510", "DRS233565", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of wild type sibling sample2", "SAMD00399012", null, "sample name:rna rw337 48hpf WT rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399012", "DRX303510", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399012", null, null, null, 26091623771.0, 86694066.0, "DRR314107", "0:150.51 1:150.45", "A:6955374552;C:6050013285;G:6169385096;T:6915281392;N:1569446", 150, 150, null, null, 6955374552, 6050013285, 6169385096, 6915281392, 1569446, "DRX303510", "DRS233565", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.94028, 0.94277, 0.11038, 0.10462, 0.68288, 0.68134, 0.46992, 0.47227, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [2, "DRR314106", "DRX303509", "DRS233564", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of wild type sibling sample1", "SAMD00399011", null, "sample name:rna rw337 48hpf WT rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399011", "DRX303509", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399011", null, null, null, 23833525756.0, 79191795.0, "DRR314106", "0:150.51 1:150.44", "A:6324521565;C:5556755459;G:5694025045;T:6256748423;N:1475264", 150, 150, null, null, 6324521565, 5556755459, 5694025045, 6256748423, 1475264, "DRX303509", "DRS233564", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.94723, 0.94975, 0.09521, 0.09114, 0.6776, 0.67819, 0.46045, 0.46153, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [3, "DRR314105", "DRX303508", "DRS233563", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of banp mutant sample3", "SAMD00399010", null, "sample name:rna rw337 48hpf Mutant rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399010", "DRX303508", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399010", null, null, null, 27688386114.0, 92009317.0, "DRR314105", "0:150.49 1:150.44", "A:7681451080;C:6071566134;G:6242782106;T:7690830655;N:1756139", 150, 150, null, null, 7681451080, 6071566134, 6242782106, 7690830655, 1756139, "DRX303508", "DRS233563", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.91038, 0.91556, 0.17971, 0.16967, 0.67718, 0.67716, 0.47042, 0.46425, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [4, "DRR314104", "DRX303507", "DRS233562", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of banp mutant sample2", "SAMD00399009", null, "sample name:rna rw337 48hpf Mutant rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399009", "DRX303507", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399009", null, null, null, 22970994572.0, 76322352.0, "DRR314104", "0:150.52 1:150.46", "A:6142535654;C:5310453740;G:5430124468;T:6086516676;N:1364034", 150, 150, null, null, 6142535654, 5310453740, 5430124468, 6086516676, 1364034, "DRX303507", "DRS233562", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.93707, 0.94063, 0.12175, 0.11613, 0.67825, 0.67649, 0.46485, 0.46905, 147, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [5, "DRR314103", "DRX303506", "DRS233561", "DRP008373", "PRJDB12134", "Comparison of expression profile between banp mutant and wildtype sibling.", "DRP008373", "Other", "To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.", null, null, null, "RNA seq of banp mutant sample1", "SAMD00399008", null, "sample name:rna rw337 48hpf Mutant rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00399008", "DRX303506", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008373", "Illumina NovaSeq 6000 paired end sequencing of SAMD00399008", null, null, null, 23637901630.0, 78541449.0, "DRR314103", "0:150.51 1:150.45", "A:6359178134;C:5420730443;G:5530700546;T:6325864263;N:1428244", 150, 150, null, null, 6359178134, 5420730443, 5530700546, 6325864263, 1428244, "DRX303506", "DRS233561", "DRA012572", "OIST|Developmental Neurobiology Unit", "Okinawa Institute of Science and Technology", 2, 0.9308, 0.93545, 0.13172, 0.12462, 0.68219, 0.6814, 0.46842, 0.46984, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2022-04-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [6, "DRR315802", "DRX305194", "DRS231989", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample4", "SAMD00400823", null, "sample name:rw147 2.5dpf wildtype  rep 4|biological replicate:4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400823", "DRX305194", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400823", null, null, null, 10262353995.0, 34151547.0, "DRR315802", "0:150.27 1:150.22", "A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550", 150, 150, null, null, 2735078560, 2386126821, 2433638250, 2707202814, 307550, "DRX305194", "DRS231989", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95231, 0.95295, 0.09229, 0.08773, 0.71819, 0.72107, 0.46746, 0.46617, 151, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [7, "DRR315801", "DRX305193", "DRS231988", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample3", "SAMD00400822", null, "sample name:rw147 2.5dpf wildtype  rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400822", "DRX305193", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400822", null, null, null, 11516368634.0, 38355888.0, "DRR315801", "0:150.15 1:150.10", "A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954", 150, 150, null, null, 3080341643, 2678048339, 2713051368, 3044449330, 477954, "DRX305193", "DRS231988", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95353, 0.95634, 0.08909, 0.08533, 0.71374, 0.71252, 0.45986, 0.46059, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [8, "DRR315800", "DRX305192", "DRS231987", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample2", "SAMD00400821", null, "sample name:rw147 2.5dpf wildtype  rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400821", "DRX305192", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400821", null, null, null, 8814057148.0, 29367513.0, "DRR315800", "0:150.09 1:150.04", "A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957", 150, 150, null, null, 2350403211, 2054073465, 2083044327, 2326181188, 354957, "DRX305192", "DRS231987", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95287, 0.95643, 0.0891, 0.08586, 0.70309, 0.70252, 0.46384, 0.46281, 151, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [9, "DRR315799", "DRX305191", "DRS231986", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample1", "SAMD00400820", null, "sample name:rw147 2.5dpf wildtype  rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400820", "DRX305191", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400820", null, null, null, 10491955578.0, 34900682.0, "DRR315799", "0:150.34 1:150.28", "A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831", 150, 150, null, null, 2796521111, 2446218287, 2483414564, 2765477785, 323831, "DRX305191", "DRS231986", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.9539, 0.95646, 0.08185, 0.07808, 0.70025, 0.70013, 0.44713, 0.44987, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [10, "DRR315798", "DRX305190", "DRS231985", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample4", "SAMD00400819", null, "sample name:rw147 2.5dpf Mutant  rep 4|biological replicate:4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400819", "DRX305190", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400819", null, null, null, 9197802250.0, 30604326.0, "DRR315798", "0:150.30 1:150.24", "A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028", 150, 150, null, null, 2468967963, 2130949980, 2158692262, 2438931017, 261028, "DRX305190", "DRS231985", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95159, 0.95439, 0.10146, 0.09758, 0.71995, 0.71983, 0.46519, 0.46797, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [11, "DRR315797", "DRX305189", "DRS231984", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample3", "SAMD00400818", null, "sample name:rw147 2.5dpf Mutant  rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400818", "DRX305189", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400818", null, null, null, 10498982078.0, 34931731.0, "DRR315797", "0:150.31 1:150.25", "A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945", 150, 150, null, null, 2804535103, 2445295179, 2478768789, 2770066062, 316945, "DRX305189", "DRS231984", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95448, 0.95652, 0.0939, 0.0887, 0.71796, 0.71847, 0.46335, 0.46615, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [12, "DRR315796", "DRX305188", "DRS231983", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample2", "SAMD00400817", null, "sample name:rw147 2.5dpf Mutant  rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400817", "DRX305188", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400817", null, null, null, 9850145990.0, 32782079.0, "DRR315796", "0:150.26 1:150.21", "A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024", 150, 150, null, null, 2636205537, 2286508705, 2319481100, 2607600624, 350024, "DRX305188", "DRS231983", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95193, 0.95472, 0.09722, 0.09375, 0.7138, 0.71299, 0.45542, 0.45994, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [13, "DRR315795", "DRX305187", "DRS231982", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample1", "SAMD00400816", null, "sample name:rw147 2.5dpf Mutant  rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400816", "DRX305187", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400816", null, null, null, 9542039835.0, 31780260.0, "DRR315795", "0:150.15 1:150.10", "A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225", 150, 150, null, null, 2543384204, 2224374632, 2258183435, 2515655339, 442225, "DRX305187", "DRS231982", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.9528, 0.95591, 0.08656, 0.0828, 0.70352, 0.70331, 0.45316, 0.44914, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [303, "DRR224539", "DRX214824", "DRS236347", "DRP008458", "PRJDB9741", "RNA seq for developing pectoral fin in zebrafish", "DRP008458", "Other", "From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.", null, null, null, "pectoral fin bud from gM1116A zebrafish at 48hpf C", "SAMD00222570", null, "sample name:48hpf C", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00222570", "DRX214824", "48hpf C", "1", "Illumina TruSeq Stranded mRNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008458", "Illumina NovaSeq 6000 paired end sequencing of SAMD00222570", null, null, null, 16828182200.0, 84140911.0, "DRR224539", "0:100 1:100", "A:3957959900;C:4467368792;G:4483580218;T:3919146988;N:126302", 100, 100, null, null, 3957959900, 4467368792, 4483580218, 3919146988, 126302, "DRX214824", "DRS236347", "DRA010086", "TOHOKUGL|Laboratory of organ morphogenesis", "Graduate School of Life Sciences, Tohoku University", 2, 0.97277, 0.97115, 0.05409, 0.05185, 0.76717, 0.76836, 0.46592, 0.45571, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2022-04-21", "Hatching", "Embryo", "Fin", "Surface Structure"], [304, "DRR224538", "DRX214823", "DRS236346", "DRP008458", "PRJDB9741", "RNA seq for developing pectoral fin in zebrafish", "DRP008458", "Other", "From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.", null, null, null, "pectoral fin bud from gM1116A zebrafish at 48hpf B", "SAMD00222569", null, "sample name:48hpf B", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00222569", "DRX214823", "48hpf B", "1", "Illumina TruSeq Stranded mRNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008458", "Illumina NovaSeq 6000 paired end sequencing of SAMD00222569", null, null, null, 22815822200.0, 114079111.0, "DRR224538", "0:100 1:100", "A:5651922913;C:5760379580;G:5844694518;T:5558658503;N:166686", 100, 100, null, null, 5651922913, 5760379580, 5844694518, 5558658503, 166686, "DRX214823", "DRS236346", "DRA010086", "TOHOKUGL|Laboratory of organ morphogenesis", "Graduate School of Life Sciences, Tohoku University", 2, 0.96814, 0.96379, 0.03526, 0.03362, 0.71575, 0.71697, 0.47605, 0.47359, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2022-04-21", "Hatching", "Embryo", "Fin", "Surface Structure"], [305, "DRR224537", "DRX214822", "DRS236345", "DRP008458", "PRJDB9741", "RNA seq for developing pectoral fin in zebrafish", "DRP008458", "Other", "From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.", null, null, null, "pectoral fin bud from gM1116A zebrafish at 48hpf A", "SAMD00222568", null, "sample name:48hpf A", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00222568", "DRX214822", "48hpf A", "1", "Illumina TruSeq Stranded mRNA Library Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008458", "Illumina NovaSeq 6000 paired end sequencing of SAMD00222568", null, null, null, 13993230400.0, 69966152.0, "DRR224537", "0:100 1:100", "A:3484590137;C:3511805255;G:3624285719;T:3372446706;N:102583", 100, 100, null, null, 3484590137, 3511805255, 3624285719, 3372446706, 102583, "DRX214822", "DRS236345", "DRA010086", "TOHOKUGL|Laboratory of organ morphogenesis", "Graduate School of Life Sciences, Tohoku University", 2, 0.96467, 0.96428, 0.04367, 0.04212, 0.72853, 0.73125, 0.49715, 0.49652, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2022-04-21", "Hatching", "Embryo", "Fin", "Surface Structure"], [10309, "ERR7179904", "ERX6749461", "ERS8138767", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1287", "SAMEA10486022", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486022|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1287|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1287|sex:mixed|stimulus:PAMP|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1287 s", "R1287 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1287_sr.fastq.gz", "fastq", 2134815688.0, 42280846.0, "E MTAB 11092:R1287", "0:50.49", "A:565052096;C:502336362;G:482125031;T:582647501;N:2654698", 50, null, null, null, 565052096, 502336362, 482125031, 582647501, 2654698, "ERX6749461", "ERS8138767", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.9356, null, 0.11997, null, 0.68314, null, 0.47934, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10310, "ERR7179903", "ERX6749460", "ERS8138766", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1284", "SAMEA10486020", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486020|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1284|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1284|sex:mixed|stimulus:water|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1284 s", "R1284 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1284_sr.fastq.gz", "fastq", 2050986060.0, 40612707.0, "E MTAB 11092:R1284", "0:50.50", "A:538161680;C:490403596;G:466089424;T:554663872;N:1667488", 50, null, null, null, 538161680, 490403596, 466089424, 554663872, 1667488, "ERX6749460", "ERS8138766", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93753, null, 0.1231, null, 0.68479, null, 0.45919, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10311, "ERR7179902", "ERX6749459", "ERS8138765", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1275", "SAMEA10486018", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486018|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1275|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1275|sex:mixed|stimulus:PAMP|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1275 s", "R1275 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1275_sr.fastq.gz", "fastq", 1157613512.0, 22947522.0, "E MTAB 11092:R1275", "0:50.45", "A:299754053;C:277899399;G:266613838;T:309994905;N:3351317", 50, null, null, null, 299754053, 277899399, 266613838, 309994905, 3351317, "ERX6749459", "ERS8138765", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.9411, null, 0.10048, null, 0.69008, null, 0.47233, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10312, "ERR7179901", "ERX6749458", "ERS8138764", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1272", "SAMEA10486016", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486016|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1272|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1272|sex:mixed|stimulus:water|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1272 s", "R1272 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:water", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1272_sr.fastq.gz", "fastq", 1634309317.0, 32374943.0, "E MTAB 11092:R1272", "0:50.48", "A:424752350;C:392450289;G:375596049;T:438931453;N:2579176", 50, null, null, null, 424752350, 392450289, 375596049, 438931453, 2579176, "ERX6749458", "ERS8138764", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93744, null, 0.10119, null, 0.68627, null, 0.47078, null, 47, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10313, "ERR7179900", "ERX6749457", "ERS8138763", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1269", "SAMEA10486014", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486014|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1269|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1269|sex:mixed|stimulus:control|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1269 s", "R1269 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1269_sr.fastq.gz", "fastq", 1209767720.0, 23959130.0, "E MTAB 11092:R1269", "0:50.49", "A:311532826;C:293995213;G:280433261;T:322310486;N:1495934", 50, null, null, null, 311532826, 293995213, 280433261, 322310486, 1495934, "ERX6749457", "ERS8138763", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.94226, null, 0.10041, null, 0.68777, null, 0.45677, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10314, "ERR7179899", "ERX6749456", "ERS8138762", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1289", "SAMEA10486012", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486012|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1289|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1289|sex:mixed|stimulus:PAMP|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1289 s", "R1289 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1289_sr.fastq.gz", "fastq", 2336898428.0, 46306897.0, "E MTAB 11092:R1289", "0:50.47", "A:612494442;C:551754242;G:532830428;T:633879257;N:5940059", 50, null, null, null, 612494442, 551754242, 532830428, 633879257, 5940059, "ERX6749456", "ERS8138762", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93744, null, 0.13096, null, 0.68753, null, 0.49027, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10315, "ERR7179898", "ERX6749455", "ERS8138761", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1286", "SAMEA10486010", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486010|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1286|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1286|sex:mixed|stimulus:water|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1286 s", "R1286 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1286_sr.fastq.gz", "fastq", 2816827872.0, 55797255.0, "E MTAB 11092:R1286", "0:50.48", "A:736348159;C:671023504;G:643914486;T:761242852;N:4298871", 50, null, null, null, 736348159, 671023504, 643914486, 761242852, 4298871, "ERX6749455", "ERS8138761", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.94033, null, 0.11711, null, 0.68477, null, 0.46969, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10316, "ERR7179897", "ERX6749454", "ERS8138760", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1277", "SAMEA10486008", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486008|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1277|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1277|sex:mixed|stimulus:PAMP|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1277 s", "R1277 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", "p946sR1277_sr.fastq.gz", "fastq", 1268705881.0, 25118834.0, "E MTAB 11092:R1277", "0:50.51 1:0", "A:329102604;C:306045954;G:293488785;T:339279603;N:788935", 50, 0, null, null, 329102604, 306045954, 293488785, 339279603, 788935, "ERX6749454", "ERS8138760", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.94045, null, 0.11288, null, 0.69025, null, 0.47095, null, 48, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10317, "ERR7179896", "ERX6749453", "ERS8138759", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1274", "SAMEA10486006", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486006|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1274|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1274|sex:mixed|stimulus:water|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1274 s", "R1274 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:water", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1274_sr.fastq.gz", "fastq", 1107133784.0, 21923109.0, "E MTAB 11092:R1274", "0:50.50", "A:289596768;C:264193186;G:253295296;T:299245790;N:802744", 50, null, null, null, 289596768, 264193186, 253295296, 299245790, 802744, "ERX6749453", "ERS8138759", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93893, null, 0.1111, null, 0.68091, null, 0.46331, null, 48, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10318, "ERR7179895", "ERX6749452", "ERS8138758", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1271", "SAMEA10486004", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486004|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1271|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T13|sample name:E MTAB 11092:R1271|sex:mixed|stimulus:control|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1271 s", "R1271 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1271_sr.fastq.gz", "fastq", 1998122568.0, 39583977.0, "E MTAB 11092:R1271", "0:50.48", "A:518205942;C:480545742;G:459346718;T:536870486;N:3153680", 50, null, null, null, 518205942, 480545742, 459346718, 536870486, 3153680, "ERX6749452", "ERS8138758", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.94252, null, 0.10542, null, 0.67886, null, 0.47083, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10319, "ERR7179894", "ERX6749451", "ERS8138757", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1288", "SAMEA10486002", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486002|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1288|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1288|sex:mixed|stimulus:PAMP|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1288 s", "R1288 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1288_sr.fastq.gz", "fastq", 1892621026.0, 37517169.0, "E MTAB 11092:R1288", "0:50.45", "A:498344488;C:444226431;G:428956415;T:514938257;N:6155435", 50, null, null, null, 498344488, 444226431, 428956415, 514938257, 6155435, "ERX6749451", "ERS8138757", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93409, null, 0.12599, null, 0.68692, null, 0.47741, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10320, "ERR7179893", "ERX6749450", "ERS8138756", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1285", "SAMEA10486000", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486000|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1285|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1285|sex:mixed|stimulus:water|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1285 s", "R1285 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1285_sr.fastq.gz", "fastq", 1829128750.0, 36225046.0, "E MTAB 11092:R1285", "0:50.49", "A:478165041;C:438683413;G:419515205;T:490751870;N:2013221", 50, null, null, null, 478165041, 438683413, 419515205, 490751870, 2013221, "ERX6749450", "ERS8138756", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93814, null, 0.11901, null, 0.68639, null, 0.46045, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10321, "ERR7179892", "ERX6749449", "ERS8138755", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1276", "SAMEA10485998", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10485998|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1276|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1276|sex:mixed|stimulus:PAMP|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1276 s", "R1276 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1276_sr.fastq.gz", "fastq", 1575013709.0, 31202630.0, "E MTAB 11092:R1276", "0:50.48", "A:406866583;C:380336879;G:364368178;T:420970851;N:2471218", 50, null, null, null, 406866583, 380336879, 364368178, 420970851, 2471218, "ERX6749449", "ERS8138755", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.9399, null, 0.10316, null, 0.68564, null, 0.45479, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10322, "ERR7179891", "ERX6749448", "ERS8138754", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1273", "SAMEA10485996", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10485996|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1273|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1273|sex:mixed|stimulus:water|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1273 s", "R1273 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:water", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1273_sr.fastq.gz", "fastq", 978769211.0, 19384726.0, "E MTAB 11092:R1273", "0:50.49", "A:254759436;C:235060632;G:224944252;T:262789193;N:1215698", 50, null, null, null, 254759436, 235060632, 224944252, 262789193, 1215698, "ERX6749448", "ERS8138754", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93731, null, 0.114, null, 0.68812, null, 0.46237, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [10323, "ERR7179890", "ERX6749447", "ERS8138753", "ERP132743", "PRJEB48372", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E-MTAB-11092", "Transcriptome Analysis", "The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate  a highly potent synthetic corticosteroid  which is known to have immunosuppressive effects on vertebrates including zebrafish  was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection  the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide  polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate.  In a modified version of the zebrafish embryo toxicity test OECD 236  20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf  the eggs were manually dechorinated. At 48 hpf  the embryos were immobilized by anaesthetization using 200 mg/mL tricaine.  Using microinjection  8 nL of the mixed PAMPs 0.33 \u00b5g/mL Pam3CSK4  0.33 \u00b5g/mL polyI:C and 0.033 \u00b5g/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs  while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection  the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25", null, "Protocols: For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the \u201cGrowth protocol\u201d. For detailed information about exposure duration and conditions please refer to the \u201cTreatment protocol\u201d. Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2\u00b0C on a 12:12 h light/dark cycle. They were fed daily with TetraMin\u00ae Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1\u00b0C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 \u00b5M in acetone before 500 \u00b5L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 \u00b5L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the \u201cgrowth protocol\u201d. Standard flagellin from Bacillus subtilis \u2248 10% purity  Pam3CSK4 \u2265 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 \u00b5L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 \u00b5L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 \u00b5m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 \u00b5g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24\u00a9 MP Biomedicals  6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/\u00b5l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer\u00a9 Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit\u00a9 Agilent  5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80\u00b0C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/\u00b5l total RNA at the sequencing facility \u201cNGS Services for Integrative Genomics\u201d at the University of G\u00f6ttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "R1270", "SAMEA10485994", "Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany", "ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10485994|INSDC center alias:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs  Fraunhofer Institute for Molecular Biology and Applied Ecology  Schmallenberg  Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1270|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T12|sample name:E MTAB 11092:R1270|sex:mixed|stimulus:control|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "E MTAB 11092:R1270 s", "R1270 s", "Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "For each sample  10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples  the supernatant was removed and the tubes were snap frozen in liquid nitrogen.   For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol.  Adult animal husbandry: Wild type zebrafish Danio rerio  Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/  2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke  Melle  Germany main feed ad libitum and nauplii of Artemia salina. The day before test start  glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking.  Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/  1C on a 14:10 h light/dark cycle. At 24 hpf  eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen  Germany. For the test solution preparation  first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H  Bandelin  Germany.  The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample  about 40   50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope  20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol.  Standard flagellin from Bacillus subtilis  10% purity  Pam3CSK4  98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse  France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water  aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf  the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs  was prepared by mixing 10 L of each component  resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4  and 0.033 mg/mL for flagellin  respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf  Hamburg  Germany  connected to an IM 300 microinjector Narishige  London  United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser  Rhede  Germany. Briefly  the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide  the output pressure was constantly kept at 10 psi  while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere  this corresponds to a volume of about 8 nL.   The procedure described below was performed for each of the five conditions in turn  treating the three replicates simultaneously. In order to anaesthetize the embryos  tricaine Sigma Aldrich Taufkirchen  Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate  which was divided into segments  one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid  if needed. To ensure that the injections could be performed as quickly as possible  the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo  where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed  the embryos were rinsed back into the corresponding dish containing renewed test solution.  Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals  6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals  6004500 at room temperature.  From here on RNA was extracted according to the manufacturers protocol.  RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent  G2939BA using the Agilent RNA 6000 Nano Kit Agilent  5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at  80C until they were send to the sequencing facility on dry ice.  Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow  cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent  Santa Clara  USA before sequencing.", "Experimental Factor: compound:n1|Experimental Factor: stimulus:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP132743", "Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos", "ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py", "p946sR1270_sr.fastq.gz", "fastq", 1079683414.0, 21379121.0, "E MTAB 11092:R1270", "0:50.50", "A:282457582;C:258094012;G:247325987;T:291030099;N:775734", 50, null, null, null, 282457582, 258094012, 247325987, 291030099, 775734, "ERX6749447", "ERS8138753", "ERA6860152", "Fraunhofer Attract Eco", "Fraunhofer Attract Eco", 1, 0.93758, null, 0.10619, null, 0.68363, null, 0.47429, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2022-01-01", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15009, "ERR12306826", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 10050750400.0, 62817190.0, "E MTAB 13554:230324 Coated S1 L003", "0:10 1:10 2:30 3:110", "A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364", 10, 10, 30, 110, 1894211982, 1556769050, 1595134885, 1863244619, 530364, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15010, "ERR12306829", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 9780757760.0, 61129736.0, "E MTAB 13554:230324 Coated S1 L004", "0:10 1:10 2:30 3:110", "A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004", 10, 10, 30, 110, 1844808667, 1516149264, 1549838165, 1813091860, 383004, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15011, "ERR12306828", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 9639368480.0, 60246053.0, "E MTAB 13554:230324 Coated S1 L002", "0:10 1:10 2:30 3:110", "A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820", 10, 10, 30, 110, 1817388578, 1494319441, 1527564319, 1787447672, 345820, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15012, "ERR12306832", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 9823147840.0, 61394674.0, "E MTAB 13554:230324 Coated S1 L001", "0:10 1:10 2:30 3:110", "A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191", 10, 10, 30, 110, 1851113558, 1521671335, 1558230628, 1822067428, 331191, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15013, "ERR12306833", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 8871716800.0, 55448230.0, "E MTAB 13554:230324 Uncoated S2 L001", "0:10 1:10 2:30 3:110", "A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567", 10, 10, 30, 110, 1718985845, 1319560520, 1372197713, 1688254655, 306567, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15014, "ERR12306830", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 9075478720.0, 56721742.0, "E MTAB 13554:230324 Uncoated S2 L003", "0:10 1:10 2:30 3:110", "A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625", 10, 10, 30, 110, 1758677834, 1349774831, 1404463433, 1725994897, 480625, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15015, "ERR12306831", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 8705210880.0, 54407568.0, "E MTAB 13554:230324 Uncoated S2 L002", "0:10 1:10 2:30 3:110", "A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916", 10, 10, 30, 110, 1687330583, 1295837902, 1345522657, 1655826422, 314916, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15016, "ERR12306827", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L004_I1_001.fastq.gz 230324-Uncoated_S2_L004_I2_001.fastq.gz 230324-Uncoated_S2_L004_R1_001.fastq.gz 230324-Uncoated_S2_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 8846203360.0, 55288771.0, "E MTAB 13554:230324 Uncoated S2 L004", "0:10 1:10 2:30 3:110", "A:1715100047;C:1316853239;G:1367208350;T:1682248092;N:355082", 10, 10, 30, 110, 1715100047, 1316853239, 1367208350, 1682248092, 355082, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [36032, "SRR33405556", "SRX28646822", "SRS24917431", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "mut2 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "mut2 d2", "mut2 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_mut-2_S6_R1_001.fastq.gz y680_mut-2_S6_R2_001.fastq.gz", "fastq fastq", 13048391588.0, 65176490.0, "y680 mut 2 S6 R1 001.fastq.gz", "0:100.12 1:100.08", "A:3382606790;C:3166963239;G:3249911967;T:3247119183;N:1790409", 100, 100, null, null, 3382606790, 3166963239, 3249911967, 3247119183, 1790409, "SRX28646822", "SRS24917431", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36033, "SRR33405557", "SRX28646821", "SRS24917430", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "mut1 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "mut1 d2", "mut1 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_mut-1_S5_R1_001.fastq.gz y680_mut-1_S5_R2_001.fastq.gz", "fastq fastq", 11244387522.0, 56145229.0, "y680 mut 1 S5 R1 001.fastq.gz", "0:100.15 1:100.12", "A:2893088657;C:2737659501;G:2830491662;T:2781546759;N:1600943", 100, 100, null, null, 2893088657, 2737659501, 2830491662, 2781546759, 1600943, "SRX28646821", "SRS24917430", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36034, "SRR33405558", "SRX28646820", "SRS24917429", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "het4 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "het4 d2", "het4 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_het-4_S4_R1_001.fastq.gz y680_het-4_S4_R2_001.fastq.gz", "fastq fastq", 7488095202.0, 37372687.0, "y680 het 4 S4 R1 001.fastq.gz", "0:100.20 1:100.16", "A:1931359037;C:1813371312;G:1880760315;T:1861860377;N:744161", 100, 100, null, null, 1931359037, 1813371312, 1880760315, 1861860377, 744161, "SRX28646820", "SRS24917429", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36035, "SRR33405559", "SRX28646819", "SRS24917428", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "het3 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "het3 d2", "het3 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_het-3_S3_R1_001.fastq.gz y680_het-3_S3_R2_001.fastq.gz", "fastq fastq", 13441009956.0, 67072919.0, "y680 het 3 S3 R1 001.fastq.gz", "0:100.22 1:100.18", "A:3484306615;C:3249847841;G:3351167195;T:3353988961;N:1699344", 100, 100, null, null, 3484306615, 3249847841, 3351167195, 3353988961, 1699344, "SRX28646819", "SRS24917428", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36036, "SRR33405560", "SRX28646818", "SRS24917427", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "het2 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "het2 d2", "het2 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_het-2_S2_R1_001.fastq.gz y680_het-2_S2_R2_001.fastq.gz", "fastq fastq", 10048330828.0, 50202819.0, "y680 het 2 S2 R1 001.fastq.gz", "0:100.10 1:100.05", "A:2557623639;C:2473642678;G:2526118363;T:2490175343;N:770805", 100, 100, null, null, 2557623639, 2473642678, 2526118363, 2490175343, 770805, "SRX28646818", "SRS24917427", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36037, "SRR33405561", "SRX28646817", "SRS24917426", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "het1 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "het1 d2", "het1 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_het-1_S1_R1_001.fastq.gz y680_het-1_S1_R2_001.fastq.gz", "fastq fastq", 21241485328.0, 106063264.0, "y680 het 1 S1 R1 001.fastq.gz", "0:100.16 1:100.11", "A:5428876256;C:5216202525;G:5316134708;T:5278092708;N:2179131", 100, 100, null, null, 5428876256, 5216202525, 5316134708, 5278092708, 2179131, "SRX28646817", "SRS24917426", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36038, "SRR33405562", "SRX28646816", "SRS24917425", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "wt4 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "wt4 d2", "wt4 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680-WT-4_S56_R1_001.fastq.gz y680-WT-4_S56_R2_001.fastq.gz", "fastq fastq", 2871774704.0, 14403351.0, "y680 WT 4 S56 R1 001.fastq.gz", "0:99.62 1:99.76", "A:738963438;C:693060627;G:725455885;T:712804013;N:1490741", 99, 99, null, null, 738963438, 693060627, 725455885, 712804013, 1490741, "SRX28646816", "SRS24917425", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36040, "SRR33405564", "SRX28646814", "SRS24917423", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "wt3 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "wt3 d2", "wt3 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_WT-3_S11_R1_001.fastq.gz y680_WT-3_S11_R2_001.fastq.gz", "fastq fastq", 4644100900.0, 23208636.0, "y680 WT 3 S11 R1 001.fastq.gz", "0:100.02 1:100.08", "A:1208863635;C:1115875593;G:1183409664;T:1134173818;N:1778190", 100, 100, null, null, 1208863635, 1115875593, 1183409664, 1134173818, 1778190, "SRX28646814", "SRS24917423", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36049, "SRR33405573", "SRX28646805", "SRS24917414", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "mut4 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "mut4 d2", "mut4 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_mut-4_S8_R1_001.fastq.gz y680_mut-4_S8_R2_001.fastq.gz", "fastq fastq", 6364246187.0, 31799210.0, "y680 mut 4 S8 R1 001.fastq.gz", "0:100.05 1:100.09", "A:1644746630;C:1536469430;G:1617907325;T:1562993280;N:2129522", 100, 100, null, null, 1644746630, 1536469430, 1617907325, 1562993280, 2129522, "SRX28646805", "SRS24917414", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36050, "SRR33405574", "SRX28646804", "SRS24917413", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "mut3 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "mut3 d2", "mut3 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_mut-3_S7_R1_001.fastq.gz y680_mut-3_S7_R2_001.fastq.gz", "fastq fastq", 12769594212.0, 63754551.0, "y680 mut 3 S7 R1 001.fastq.gz", "0:100.17 1:100.12", "A:3270488183;C:3128646350;G:3212521095;T:3156861188;N:1077396", 100, 100, null, null, 3270488183, 3128646350, 3212521095, 3156861188, 1077396, "SRX28646804", "SRS24917413", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36051, "SRR33405575", "SRX28646803", "SRS24917412", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "wt2 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "wt2 d2", "wt2 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680-WT-2_S40_R1_001.fastq.gz y680-WT-2_S40_R2_001.fastq.gz", "fastq fastq", 7228768016.0, 36426014.0, "y680 WT 2 S40 R1 001.fastq.gz", "0:99.18 1:99.27", "A:1808349692;C:1804255213;G:1817770107;T:1795596464;N:2796540", 99, 99, null, null, 1808349692, 1804255213, 1817770107, 1795596464, 2796540, "SRX28646803", "SRS24917412", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [36052, "SRR33405576", "SRX28646802", "SRS24917411", "SRP582714", "PRJNA1257950", "Zebrafish Timothy syndrome knock in model", "PRJNA1257950", "Other", "Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.", null, null, null, null, "wt1 d2", null, "strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish TS2 mutant", "wt1 d2", "wt1 d2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP582714", null, null, "y680_WT-1_S9_R1_001.fastq.gz y680_WT-1_S9_R2_001.fastq.gz", "fastq fastq", 6639999850.0, 33169283.0, "y680 WT 1 S9 R1 001.fastq.gz", "0:100.08 1:100.10", "A:1706100512;C:1614640504;G:1665440844;T:1651930739;N:1887251", 100, 100, null, null, 1706100512, 1614640504, 1665440844, 1651930739, 1887251, "SRX28646802", "SRS24917411", "SRA2122396", "NICHD|DDB", "NICHD", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2025-05-01", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [38119, "SRR1551796", "SRX681416", "SRS685079", "SRP045504", "PRJNA258223", "Danio rerio strain:TL Transcriptome or Gene expression", "PRJNA258223", "Other", "Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos", null, null, null, "Transcriptome from 2dpf keratocytes", "keratocytes from 2dpf embryos", null, "breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot  Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome from 2dpf keratocytes  replicate 3", "2dpf 3", "2dpf 3", "RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen.  Three biological replicates were collected for each developmental stage.  Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre.  The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate  1mM EDTA  pH 9.2 at 95 degrees.  To prepare cDNA  first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming  and second strand synthesis was performed with DNA Polymerase I NEB.  Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter.  Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer\u2019s instructions to generate 40nt single ended reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP045504", null, null, "lane3_2dpf629.fastq", "fastq", 551787520.0, 13794688.0, "2dpf 3", "0:40", "A:138660463;C:132605577;G:134640312;T:145852714;N:28454", 40, null, null, null, 138660463, 132605577, 134640312, 145852714, 28454, "SRX681416", "SRS685079", "SRA179323", "Stanford University|Julie Theriot", "Stanford University", 1, 0.91375, null, 0.21598, null, 0.75317, null, 0.47881, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-08-14", "Hatching", "Embryo", "Skin", "Surface Structure"], [38120, "SRR1551795", "SRX681415", "SRS685079", "SRP045504", "PRJNA258223", "Danio rerio strain:TL Transcriptome or Gene expression", "PRJNA258223", "Other", "Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos", null, null, null, "Transcriptome from 2dpf keratocytes", "keratocytes from 2dpf embryos", null, "breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot  Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome from 2dpf keratocytes", "2dpf 2", "2dpf 2", "RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen.  Three biological replicates were collected for each developmental stage.  Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre.  The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate  1mM EDTA  pH 9.2 at 95 degrees.  To prepare cDNA  first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming  and second strand synthesis was performed with DNA Polymerase I NEB.  Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter.  Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer\u2019s instructions to generate 40nt single ended reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP045504", null, null, "lane1_2dpf.fastq", "fastq", 796874112.0, 22135392.0, "2dpf 2", "0:36", "A:209956517;C:184659684;G:185142987;T:216055902;N:1059022", 36, null, null, null, 209956517, 184659684, 185142987, 216055902, 1059022, "SRX681415", "SRS685079", "SRA179323", "Stanford University|Julie Theriot", "Stanford University", 1, 0.89178, null, 0.17837, null, 0.7609, null, 0.49774, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2015-04-07", "Hatching", "Embryo", "Skin", "Surface Structure"], [38121, "SRR1551782", "SRX681402", "SRS685079", "SRP045504", "PRJNA258223", "Danio rerio strain:TL Transcriptome or Gene expression", "PRJNA258223", "Other", "Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos", null, null, null, "Transcriptome from 2dpf keratocytes", "keratocytes from 2dpf embryos", null, "breed:TL|strain:TL|age:2dpf|biomaterial provider:Julie Theriot  Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:2dpf|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "2dpf keratocytes  replicate 1", "2dpf 1", "2dpf 1", "RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen.  Three biological replicates were collected for each developmental stage.  Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre.  The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate  1mM EDTA  pH 9.2 at 95 degrees.  To prepare cDNA  first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming  and second strand synthesis was performed with DNA Polymerase I NEB.  Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter.  Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer\u2019s instructions to generate 40nt single ended reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP045504", null, null, "lane6_2dpf.fastq", "fastq", 647944118.0, 17051161.0, "2dpf 1", "0:38", "A:145735255;C:167786338;G:186677806;T:141598169;N:6146550", 38, null, null, null, 145735255, 167786338, 186677806, 141598169, 6146550, "SRX681402", "SRS685079", "SRA179323", "Stanford University|Julie Theriot", "Stanford University", 1, 0.7695, null, 0.15816, null, 0.81491, null, 0.44972, null, 38, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-08-14", "Hatching", "Embryo", "Skin", "Surface Structure"], [55877, "SRR10863019", "SRX7533050", "SRS5972252", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 2dpf", "imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6", "imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R2.fastq.gz", "fastq fastq", 3108720942.0, 19675449.0, "imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6.R1.fastq.gz", "0:79 1:79", "A:837919918;C:714812252;G:702998193;T:852776390;N:214189", 79, 79, null, null, 837919918, 714812252, 702998193, 852776390, 214189, "SRX7533050", "SRS5972252", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93952, 0.93945, 0.07277, 0.07278, 0.66983, 0.67221, 0.50192, 0.50133, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55878, "SRR10863020", "SRX7533049", "SRS5972244", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 2dpf", "imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5", "imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R2.fastq.gz", "fastq fastq", 3241530370.0, 20516015.0, "imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5.R1.fastq.gz", "0:79 1:79", "A:861911078;C:762577918;G:730686512;T:886132359;N:222503", 79, 79, null, null, 861911078, 762577918, 730686512, 886132359, 222503, "SRX7533049", "SRS5972244", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93797, 0.93734, 0.06416, 0.06415, 0.67004, 0.67251, 0.50367, 0.50353, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55879, "SRR10863021", "SRX7533048", "SRS5972269", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 2dpf", "imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4", "imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R2.fastq.gz", "fastq fastq", 3363342524.0, 21286978.0, "imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4.R1.fastq.gz", "0:79 1:79", "A:906938869;C:772810568;G:756589497;T:926768184;N:235406", 79, 79, null, null, 906938869, 772810568, 756589497, 926768184, 235406, "SRX7533048", "SRS5972269", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93588, 0.93667, 0.11457, 0.11483, 0.66663, 0.66799, 0.4795, 0.4762, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55893, "SRR10863034", "SRX7533034", "SRS5972259", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 2dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 2dpf", "imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16", "imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R2.fastq.gz", "fastq fastq", 3091658206.0, 19567457.0, "imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16.R1.fastq.gz", "0:79 1:79", "A:818837054;C:727836511;G:707557580;T:837216941;N:210120", 79, 79, null, null, 818837054, 727836511, 707557580, 837216941, 210120, "SRX7533034", "SRS5972259", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94667, 0.94646, 0.08702, 0.08692, 0.69804, 0.70138, 0.43628, 0.43409, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55894, "SRR10863035", "SRX7533033", "SRS5972258", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 2dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 2dpf", "imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15", "imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R2.fastq.gz", "fastq fastq", 3499876328.0, 22151116.0, "imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15.R1.fastq.gz", "0:79 1:79", "A:931187812;C:820606968;G:796104654;T:951733888;N:243006", 79, 79, null, null, 931187812, 820606968, 796104654, 951733888, 243006, "SRX7533033", "SRS5972258", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94532, 0.94537, 0.10394, 0.10459, 0.69489, 0.69727, 0.4345, 0.43676, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59036, "SRR11578951", "SRX8146805", "SRS6509417", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "WT", "54WT4", "54WT4", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT4 R1 001.fastq.gz|filename2:54WT4 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54WT4", "S7", "S7", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54WT4_R2_001.fastq.gz 54WT4_R1_001.fastq.gz", "fastq fastq", 7136583059.0, 47328719.0, "54WT4 R1 001.fastq.gz", "0:75.39 1:75.40", "A:1980254600;C:1593971374;G:1644375041;T:1916731613;N:1250431", 75, 75, null, null, 1980254600, 1593971374, 1644375041, 1916731613, 1250431, "SRX8146805", "SRS6509417", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.91504, 0.91439, 0.09602, 0.09527, 0.73245, 0.73777, 0.46955, 0.48655, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59037, "SRR11578952", "SRX8146804", "SRS6509416", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "WT", "54WT3", "54WT3", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT3 R1 001.fastq.gz|filename2:54WT3 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54WT3", "S5", "S5", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54WT3_R1_001.fastq.gz 54WT3_R2_001.fastq.gz", "fastq fastq", 5683476624.0, 37713746.0, "54WT3 R1 001.fastq.gz", "0:75.35 1:75.35", "A:1578885174;C:1271523804;G:1309222456;T:1522827535;N:1017655", 75, 75, null, null, 1578885174, 1271523804, 1309222456, 1522827535, 1017655, "SRX8146804", "SRS6509416", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.91126, 0.91193, 0.10356, 0.10472, 0.73975, 0.7461, 0.47619, 0.47737, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59038, "SRR11578953", "SRX8146803", "SRS6509415", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "WT", "54WT2", "54WT2", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT2 R1 001.fastq.gz|filename2:54WT2 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54WT2", "S3", "S3", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54WT2_R1_001.fastq.gz 54WT2_R2_001.fastq.gz", "fastq fastq", 6860136869.0, 45523385.0, "54WT2 R1 001.fastq.gz", "0:75.34 1:75.35", "A:1906640944;C:1530528609;G:1580010044;T:1841799217;N:1158055", 75, 75, null, null, 1906640944, 1530528609, 1580010044, 1841799217, 1158055, "SRX8146803", "SRS6509415", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.91215, 0.91207, 0.10861, 0.11028, 0.74381, 0.74968, 0.48908, 0.49262, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59039, "SRR11578954", "SRX8146802", "SRS6509414", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "WT", "54WT1", "54WT1", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT1 R1 001.fastq.gz|filename2:54WT1 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54WT1", "S1", "S1", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54WT1_R1_001.fastq.gz 54WT1_R2_001.fastq.gz", "fastq fastq", 6225284142.0, 41319897.0, "54WT1 R1 001.fastq.gz", "0:75.33 1:75.33", "A:1729358086;C:1392766589;G:1430690093;T:1671396108;N:1073266", 75, 75, null, null, 1729358086, 1392766589, 1430690093, 1671396108, 1073266, "SRX8146802", "SRS6509414", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.92733, 0.92867, 0.09387, 0.09333, 0.71163, 0.71494, 0.486, 0.48867, 72, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59040, "SRR11578955", "SRX8146801", "SRS6509413", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "Clo", "54Clo4", "54Clo4", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo4 R1 001.fastq.gz|filename2:54Clo4 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54Clo4", "S8", "S8", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54Clo4_R1_001.fastq.gz 54Clo4_R2_001.fastq.gz", "fastq fastq", 6770856878.0, 44915858.0, "54Clo4 R1 001.fastq.gz", "0:75.37 1:75.38", "A:1876646232;C:1514408795;G:1561029116;T:1817557290;N:1215445", 75, 75, null, null, 1876646232, 1514408795, 1561029116, 1817557290, 1215445, "SRX8146801", "SRS6509413", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.91659, 0.91674, 0.10388, 0.10458, 0.71948, 0.72523, 0.48917, 0.4856, 76, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59041, "SRR11578956", "SRX8146800", "SRS6509412", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "Clo", "54Clo3", "54Clo3", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo3 R1 001.fastq.gz|filename2:54Clo3 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54Clo3", "S6", "S6", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54Clo3_R2_001.fastq.gz 54Clo3_R1_001.fastq.gz", "fastq fastq", 5822390786.0, 38650567.0, "54Clo3 R1 001.fastq.gz", "0:75.32 1:75.32", "A:1619353584;C:1299190067;G:1337336722;T:1565486844;N:1023569", 75, 75, null, null, 1619353584, 1299190067, 1337336722, 1565486844, 1023569, "SRX8146800", "SRS6509412", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.91509, 0.91425, 0.10591, 0.10604, 0.76386, 0.7693, 0.46813, 0.46524, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59042, "SRR11578957", "SRX8146799", "SRS6509411", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "Clo", "54Clo2", "54Clo2", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo2 R1 001.fastq.gz|filename2:54Clo2 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54Clo2", "S4", "S4", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54Clo2_R2_001.fastq.gz 54Clo2_R1_001.fastq.gz", "fastq fastq", 6138626977.0, 40727824.0, "54Clo2 R1 001.fastq.gz", "0:75.36 1:75.36", "A:1700144556;C:1378599434;G:1420945150;T:1637894336;N:1043501", 75, 75, null, null, 1700144556, 1378599434, 1420945150, 1637894336, 1043501, "SRX8146799", "SRS6509411", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.90602, 0.90662, 0.09596, 0.09691, 0.75872, 0.76274, 0.48174, 0.48196, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [59043, "SRR11578958", "SRX8146798", "SRS6509410", "SRP257662", "PRJNA627095", "Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf", "PRJNA627095", "Other", "In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.", null, null, "Clo", "54Clo1", "54Clo1", null, "strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo1 R1 001.fastq.gz|filename2:54Clo1 R2 001.fastq.gz|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "54Clo1", "S2", "S2", "low input mRNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP257662", null, null, "54Clo1_R1_001.fastq.gz 54Clo1_R2_001.fastq.gz", "fastq fastq", 7414571165.0, 49175642.0, "54Clo1 R1 001.fastq.gz", "0:75.39 1:75.39", "A:2056892212;C:1660481957;G:1708780731;T:1987161426;N:1254839", 75, 75, null, null, 2056892212, 1660481957, 1708780731, 1987161426, 1254839, "SRX8146798", "SRS6509410", "SRA1067518", "UPF|Genomics", "UPF", 2, 0.90938, 0.91029, 0.1024, 0.1024, 0.73507, 0.73852, 0.48964, 0.48917, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2020-04-21", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"]], "truncated": false, "filtered_table_rows_count": 68, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.library_selection\" = :p1 order by rowid limit 101", "params": {"p0": "Hatching", "p1": "PolyA"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 60, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "PolyA", "label": "PolyA", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 50, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 18, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "Embryo", "label": "Embryo", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "Hatching", "label": "Hatching", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation_coarse=Embryo+Imprecise", "selected": false}, {"value": "All anatomical structures", "label": "All anatomical structures", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Surface Structure", "label": "Surface Structure", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation=Undetermined", "selected": false}, {"value": "Whole Organism", "label": "Whole Organism", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation=Whole+Organism", "selected": false}, {"value": "Fin", "label": "Fin", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation=Fin", "selected": false}, {"value": "Skin", "label": "Skin", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&tissue_curation=Skin", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA", "results": [{"value": "unknown", "label": "unknown", "count": 47, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&technology=unknown", "selected": false}, {"value": "10x", "label": "10x", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&technology=10x", "selected": false}, {"value": "bulk", "label": "bulk", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&technology=bulk", "selected": false}, {"value": "smartseq", "label": "smartseq", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_selection=PolyA&technology=smartseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 122.22454899983859}