{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.platform = \"ION_TORRENT\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[41404, "SRR4423134", "SRX2245318", "SRS1745863", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 10 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 16 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: prim 16 stage31 hpf", "347 10", "347 10", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S10large.fastq", "fastq", 641713718.0, 5457079.0, "S10large.fastq", "0:117.59", "A:150550840;C:168565594;G:198254445;T:124342839;N:0", 117, null, null, null, 150550840, 168565594, 198254445, 124342839, 0, "SRX2245318", "SRS1745863", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.94199, null, 0.27559, null, 0.93772, null, 0.79623, null, 104, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41405, "SRR4423133", "SRX2245317", "SRS1745862", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 9 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 5 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: prim 5 stage24 hpf", "347 9", "347 9", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S09large.fastq", "fastq", 583272900.0, 4872369.0, "S09large.fastq", "0:119.71", "A:133536706;C:155614585;G:187341444;T:106780165;N:0", 119, null, null, null, 133536706, 155614585, 187341444, 106780165, 0, "SRX2245317", "SRS1745862", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.96394, null, 0.25145, null, 0.95785, null, 0.77358, null, 147, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41406, "SRR4423130", "SRX2245314", "SRS1745863", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 10 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 16 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: prim 16 stage31 hpf", "348 10", "348 10", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. 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A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. 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A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. 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"RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S02large.fastq", "fastq", 399030043.0, 3512248.0, "S02large.fastq", "0:113.61", "A:91615111;C:108172506;G:123312384;T:75930042;N:0", 113, null, null, null, 91615111, 108172506, 123312384, 75930042, 0, "SRX2245304", "SRS1745852", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.92466, null, 0.24175, null, 0.94197, null, 0.89366, null, 92, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41417, "SRR4423119", "SRX2245303", "SRS1745853", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 1 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:64 cells|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: 64 cells2 hpf", "347 1", "347 1", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S01large.fastq", "fastq", 406838773.0, 3451573.0, "S01large.fastq", "0:117.87", "A:90440106;C:114282886;G:115318720;T:86797061;N:0", 117, null, null, null, 90440106, 114282886, 115318720, 86797061, 0, "SRX2245303", "SRS1745853", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.9203, null, 0.10547, null, 0.93095, null, 0.75003, null, 158, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41428, "SRR4423108", "SRX2245292", "SRS1745857", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 5 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:90% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 90% epiboly stage 9 hpf", "348 5", "348 5", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S05small.fastq", "fastq", 412237561.0, 3386443.0, "S05small.fastq", "0:121.73", "A:91644321;C:118905395;G:115070912;T:86616933;N:0", 121, null, null, null, 91644321, 118905395, 115070912, 86616933, 0, "SRX2245292", "SRS1745857", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81233, null, 0.06309, null, 0.93385, null, 0.93973, null, 163, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41429, "SRR4423107", "SRX2245291", "SRS1745856", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 6 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:4 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 4 somite stage11.3 hpf", "348 6", "348 6", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S06small.fastq", "fastq", 535288776.0, 4443685.0, "S06small.fastq", "0:120.46", "A:119322177;C:152704452;G:149509408;T:113752739;N:0", 120, null, null, null, 119322177, 152704452, 149509408, 113752739, 0, "SRX2245291", "SRS1745856", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.82872, null, 0.09035, null, 0.93194, null, 0.81296, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41430, "SRR4423106", "SRX2245290", "SRS1745854", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 3 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:zfs:0000015 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf", "348 3", "348 3", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S03small.fastq", "fastq", 1025732824.0, 7452991.0, "S03small.fastq", "0:137.63", "A:225573059;C:298586545;G:288470386;T:213102834;N:0", 137, null, null, null, 225573059, 298586545, 288470386, 213102834, 0, "SRX2245290", "SRS1745854", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.8983, null, 0.04271, null, 0.95546, null, 0.91281, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41431, "SRR4423105", "SRX2245289", "SRS1745855", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 4 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:70% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 70% epiboly stage7 hpf", "348 4", "348 4", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S04small.fastq", "fastq", 193259658.0, 1840126.0, "S04small.fastq", "0:105.03", "A:43516548;C:54669405;G:53501927;T:41571778;N:0", 105, null, null, null, 43516548, 54669405, 53501927, 41571778, 0, "SRX2245289", "SRS1745855", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81053, null, 0.16265, null, 0.90698, null, 0.92112, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41432, "SRR4423104", "SRX2245288", "SRS1745853", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 1 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:64 cells|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 64 cells2 hpf", "348 1", "348 1", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S01small.fastq", "fastq", 91910627.0, 1396009.0, "S01small.fastq", "0:65.84", "A:21663404;C:25661192;G:25069267;T:19516764;N:0", 65, null, null, null, 21663404, 25661192, 25069267, 19516764, 0, "SRX2245288", "SRS1745853", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.56828, null, 0.1715, null, 0.92435, null, 0.90047, null, 34, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41433, "SRR4423103", "SRX2245287", "SRS1745852", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 2 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:high stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: high stage3.3 hpf", "348 2", "348 2", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S02small.fastq", "fastq", 304535574.0, 3376105.0, "S02small.fastq", "0:90.20", "A:69193719;C:84372087;G:86707481;T:64262287;N:0", 90, null, null, null, 69193719, 84372087, 86707481, 64262287, 0, "SRX2245287", "SRS1745852", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.56812, null, 0.09695, null, 0.93474, null, 0.93654, null, 51, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41434, "SRR4423102", "SRX2245286", "SRS1745851", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 11 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:long pec stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: long pec stage48 hpf", "347 11", "347 11", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S11large.fastq", "fastq", 535498199.0, 5737354.0, "S11large.fastq", "0:93.34", "A:121755741;C:143034204;G:168067337;T:102640917;N:0", 93, null, null, null, 121755741, 143034204, 168067337, 102640917, 0, "SRX2245286", "SRS1745851", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.9065, null, 0.26226, null, 0.9388, null, 0.73978, null, 95, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41435, "SRR4423101", "SRX2245285", "SRS1745850", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 12 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:protruding mouth stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Zebrafish: protruding mouth stage72 hpf", "347 12", "347 12", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S12large.fastq", "fastq", 2735647095.0, 28978873.0, "S12large.fastq", "0:94.40", "A:650857562;C:721265476;G:776126849;T:587397208;N:0", 94, null, null, null, 650857562, 721265476, 776126849, 587397208, 0, "SRX2245285", "SRS1745850", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.87809, null, 0.18943, null, 0.88797, null, 0.71439, null, 27, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [41436, "SRR4423100", "SRX2245284", "SRS1745849", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 7 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:12 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 12 somite stage15 hpf", "348 7", "348 7", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S07small.fastq", "fastq", 279201769.0, 2713759.0, "S07small.fastq", "0:102.88", "A:61655863;C:78667355;G:77702440;T:61176111;N:0", 102, null, null, null, 61655863, 78667355, 77702440, 61176111, 0, "SRX2245284", "SRS1745849", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.79087, null, 0.10046, null, 0.89221, null, 0.77892, null, 158, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41437, "SRR4423099", "SRX2245283", "SRS1745848", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 8 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:22 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 22 somite stage20 hpf", "348 8", "348 8", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S08small.fastq", "fastq", 520785540.0, 4495080.0, "S08small.fastq", "0:115.86", "A:115224831;C:149325753;G:144978190;T:111256766;N:0", 115, null, null, null, 115224831, 149325753, 144978190, 111256766, 0, "SRX2245283", "SRS1745848", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.83781, null, 0.08976, null, 0.92904, null, 0.80492, null, 183, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62959, "SRR13520382", "SRX9931400", "SRS8106885", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "G8 12: pEGFP N1 injected at 12hpf", "GSM5033117", null, "source name:zebrafish embryos|strain:TU|developmental stage:12hpf|tissue:embryo", "G8 12: pEGFP N1 injected at 12hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:12hpf|tissue:embryo", "GSM5033117", "GSM5033117: G8 12: pEGFP N1 injected at 12hpf; Danio rerio; RNA Seq", "GSM5033117", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "G8-12.fastq.gz", "fastq", 2163053937.0, 12776614.0, "GSM5033117 r1", "0:169.30", "A:581602408;C:540446105;G:566494100;T:474511324;N:0", 169, null, null, null, 581602408, 540446105, 566494100, 474511324, 0, "SRX9931400", "SRS8106885", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.73901, null, 0.01942, null, 0.7726, null, 0.47694, null, 169, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62960, "SRR13520381", "SRX9931399", "SRS8106884", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "G8 6: pEGFP N1 injected at 6pf", "GSM5033116", null, "source name:zebrafish embryos|strain:TU|developmental stage:6pf|tissue:embryo", "G8 6: pEGFP N1 injected at 6pf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:6pf|tissue:embryo", "GSM5033116", "GSM5033116: G8 6: pEGFP N1 injected at 6pf; Danio rerio; RNA Seq", "GSM5033116", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "G8-6.fastq.gz", "fastq", 2116443238.0, 12869630.0, "GSM5033116 r1", "0:164.45", "A:580007846;C:516340658;G:549230787;T:470863947;N:0", 164, null, null, null, 580007846, 516340658, 549230787, 470863947, 0, "SRX9931399", "SRS8106884", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.73674, null, 0.02266, null, 0.79722, null, 0.49168, null, 119, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62961, "SRR13520380", "SRX9931398", "SRS8106883", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "G8 1: pEGFP N1 injected at 1hpf", "GSM5033115", null, "source name:zebrafish embryos|strain:TU|developmental stage:1hpf|tissue:embryo", "G8 1: pEGFP N1 injected at 1hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:1hpf|tissue:embryo", "GSM5033115", "GSM5033115: G8 1: pEGFP N1 injected at 1hpf; Danio rerio; RNA Seq", "GSM5033115", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "G8-1.fastq.gz", "fastq", 2029634086.0, 12394054.0, "GSM5033115 r1", "0:163.76", "A:548662597;C:501840467;G:525047427;T:454083595;N:0", 163, null, null, null, 548662597, 501840467, 525047427, 454083595, 0, "SRX9931398", "SRS8106883", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.81344, null, 0.01015, null, 0.78058, null, 0.48067, null, 90, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62962, "SRR13520379", "SRX9931397", "SRS8106882", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "C12: un injected at 12hpf", "GSM5033114", null, "source name:zebrafish embryos|strain:TU|developmental stage:12hpf|tissue:embryo", "C12: un injected at 12hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:12hpf|tissue:embryo", "GSM5033114", "GSM5033114: C12: un injected at 12hpf; Danio rerio; RNA Seq", "GSM5033114", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "C12.fastq.gz", "fastq", 2287177824.0, 14569411.0, "GSM5033114 r1", "0:156.98", "A:618744606;C:567027488;G:600125143;T:501280587;N:0", 156, null, null, null, 618744606, 567027488, 600125143, 501280587, 0, "SRX9931397", "SRS8106882", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.74656, null, 0.02098, null, 0.76928, null, 0.47392, null, 184, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62963, "SRR13520378", "SRX9931396", "SRS8106881", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "C6: un injected at 6pf", "GSM5033113", null, "source name:zebrafish embryos|strain:TU|developmental stage:6pf|tissue:embryo", "C6: un injected at 6pf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:6pf|tissue:embryo", "GSM5033113", "GSM5033113: C6: un injected at 6pf; Danio rerio; RNA Seq", "GSM5033113", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "C6.fastq.gz", "fastq", 1998132252.0, 12473595.0, "GSM5033113 r1", "0:160.19", "A:548408269;C:485097126;G:517913632;T:446713225;N:0", 160, null, null, null, 548408269, 485097126, 517913632, 446713225, 0, "SRX9931396", "SRS8106881", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.73967, null, 0.02632, null, 0.79482, null, 0.48895, null, 160, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62964, "SRR13520377", "SRX9931395", "SRS8106880", "SRP303129", "PRJNA694577", "Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes", "GSE165422", "Transcriptome Analysis", "Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT\u2013PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection  and then when the embryos to develop ttwo xxx hpf  6 hpf and 12 hpf  these groups was collected respectively by deep sequencing  in triplicate  using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows\u2013Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT\u2013PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A  endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation  mainly including isg15  foxo3b  phlda3  cdkn1a  zgc:136826  and si:dkey 204l11.1  compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf  6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group", null, "pubmed:35690839", null, "C1: un injected at 1hpf", "GSM5033112", null, "source name:zebrafish embryos|strain:TU|developmental stage:1hpf|tissue:embryo", "C1: un injected at 1hpf", "Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10  genome using Mapsplice v2.1.8 with  parameters  s 22  p 15   ins 6   del 6   non canonical   bam  o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample", "zebrafish embryos", "In the 1 cell stage of zebrafish embryos  8ng/\u03bcL pEGFP N1 was injected  and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf  6hpf and 12hpf. Add 1mL TRIzol Invitrogen  USA  store at  80\u2103", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", null, "strain:TU|developmental stage:1hpf|tissue:embryo", "GSM5033112", "GSM5033112: C1: un injected at 1hpf; Danio rerio; RNA Seq", "GSM5033112", null, "1", "RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol", "GEO Accession:GSM5033112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP303129", null, null, "C1.fastq.gz", "fastq", 2073298475.0, 13102880.0, "GSM5033112 r1", "0:158.23", "A:558146987;C:513562209;G:538130597;T:463458682;N:0", 158, null, null, null, 558146987, 513562209, 538130597, 463458682, 0, "SRX9931395", "SRS8106880", "SRA1187495", "GEO", "Qingshun Zhao", 1, 0.83706, null, 0.01172, null, 0.77948, null, 0.48172, null, 233, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2021-01-25", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75396, "SRR24497420", "SRX20282374", "SRS17609397", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate3", "GSM7321058", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate3", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321058", "GSM7321058: Mcpip1 DN replicate3; Danio rerio; RNA Seq", "GSM7321058 r1", "GSM7321058", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_C24.fastq.gz", "fastq", 4215951250.0, 27509986.0, "GSM7321058 r1", "0:153.25", "A:1174686445;C:999279135;G:1076390086;T:965595584;N:0", 153, null, null, null, 1174686445, 999279135, 1076390086, 965595584, 0, "SRX20282374", "SRS17609397", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.7271, null, 0.04079, null, 0.77583, null, 0.48331, null, 128, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75397, "SRR24497423", "SRX20282373", "SRS17609396", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate2", "GSM7321057", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate2", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321057", "GSM7321057: Mcpip1 DN replicate2; Danio rerio; RNA Seq", "GSM7321057 r1", "GSM7321057", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_B16.fastq.gz", "fastq", 4150646040.0, 29771678.0, "GSM7321057 r1", "0:139.42", "A:1158168842;C:981804106;G:1077873702;T:932799390;N:0", 139, null, null, null, 1158168842, 981804106, 1077873702, 932799390, 0, "SRX20282373", "SRS17609396", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.83432, null, 0.03292, null, 0.77068, null, 0.48489, null, 149, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75398, "SRR24497421", "SRX20282372", "SRS17609394", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 DN replicate1", "GSM7321056", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing", "Mcpip1 DN replicate1", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N", "GSM7321056", "GSM7321056: Mcpip1 DN replicate1; Danio rerio; RNA Seq", "GSM7321056 r1", "GSM7321056", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "DN_A8.fastq.gz", "fastq", 3405374389.0, 22617333.0, "GSM7321056 r1", "0:150.56", "A:943415180;C:825787941;G:885910600;T:750260668;N:0", 150, null, null, null, 943415180, 825787941, 885910600, 750260668, 0, "SRX20282372", "SRS17609394", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.85916, null, 0.04442, null, 0.78344, null, 0.48648, null, 177, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75399, "SRR24497422", "SRX20282371", "SRS17609395", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 WT replicate3", "GSM7321055", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing", "Mcpip1 WT replicate3", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1", "GSM7321055", "GSM7321055: Mcpip1 WT replicate3; Danio rerio; RNA Seq", "GSM7321055 r1", "GSM7321055", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "WT_C23.fastq.gz", "fastq", 3644157793.0, 27473010.0, "GSM7321055 r1", "0:132.65", "A:1014320322;C:878841963;G:948316248;T:802679260;N:0", 132, null, null, null, 1014320322, 878841963, 948316248, 802679260, 0, "SRX20282371", "SRS17609395", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.88531, null, 0.03151, null, 0.75101, null, 0.49337, null, 123, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75400, "SRR24497424", "SRX20282370", "SRS17609393", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 WT replicate2", "GSM7321054", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing", "Mcpip1 WT replicate2", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1", "GSM7321054", "GSM7321054: Mcpip1 WT replicate2; Danio rerio; RNA Seq", "GSM7321054 r1", "GSM7321054", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "WT_B15.fastq.gz", "fastq", 4930632556.0, 30493682.0, "GSM7321054 r1", "0:161.69", "A:1385638764;C:1206486517;G:1269832302;T:1068674973;N:0", 161, null, null, null, 1385638764, 1206486517, 1269832302, 1068674973, 0, "SRX20282370", "SRS17609393", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.86405, null, 0.03935, null, 0.78324, null, 0.49971, null, 107, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"], [75401, "SRR24497425", "SRX20282369", "SRS17609392", "SRP436940", "PRJNA971233", "MCPIP1 functions as a safeguard of early embryonic development", "GSE232220", "Transcriptome Analysis", "Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.", null, "pubmed:37805647", null, "Mcpip1 WT replicate1", "GSM7321053", null, "source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing", "Mcpip1 WT replicate1", "Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a  PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700  using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count", "embryo 6 hpf", "Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", "AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28\u00b0C according to standard protocols.", "tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1", "GSM7321053", "GSM7321053: Mcpip1 WT replicate1; Danio rerio; RNA Seq", "GSM7321053 r1", "GSM7321053", "1", "Zebrafish embryos were collected in Fenozol A&A Biotechnology  Gdansk  Polska and stored at  80\u00b0C  prior to analysis. For RNA isolation  the samples were homogenized in Fenozol using a tissue homogenizer OMNI International  Kennesaw  GA  USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads\u00ae mRNA DIRECT\u2122 Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII  purifying the fragmented RNA  and hybridizing and ligating it with Ion adaptors. Subsequently  the RNA products were reverse transcribed and amplified to double stranded cDNA  and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP436940", null, null, "WT_A7.fastq.gz", "fastq", 4888312783.0, 29414563.0, "GSM7321053 r1", "0:166.19", "A:1356799075;C:1172146709;G:1273947582;T:1085419417;N:0", 166, null, null, null, 1356799075, 1172146709, 1273947582, 1085419417, 0, "SRX20282369", "SRS17609392", "SRA1636184", "Genetics, Maria Sklodowska-Curie National Research Institute of Oncology", "Genetics, Maria Sk\u0142odowska-Curie National Research Institute of Oncology", 1, 0.82661, null, 0.05547, null, 0.7751, null, 0.49668, null, 188, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Poland", "2023-05-10", "Multi-stage", "Multi-stage", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 36, "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 \"experiment.library_selection\" = :p0 and \"experiment.platform\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "cDNA", "p1": "ION_TORRENT", "p2": "Embryo Imprecise"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "cDNA", "label": "cDNA", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&tissue_curation=Embryo+Imprecise", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "Embryo", "label": "Embryo", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Larval", "label": "Larval", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation_coarse=Larval", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Multi-stage", "selected": false}, {"value": "Segmentation", "label": "Segmentation", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Segmentation", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Blastula", "selected": false}, {"value": "Cleavage", "label": "Cleavage", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Cleavage", "selected": false}, {"value": "Gastrula", "label": "Gastrula", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Gastrula", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Pharyngula", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Hatching", "selected": false}, {"value": "Larval", "label": "Larval", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&devstage_curation=Larval", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise", "results": [{"value": "unknown", "label": "unknown", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&experiment.platform=ION_TORRENT&tissue_curation=Embryo+Imprecise&technology=bulk", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 113.59263100166572}