{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", tissue_curation = \"Head\" and tissue_curation_coarse = \"Nervous System\"", "rows": [[10407, "ERR9077202", "ERX8620336", "ERS10857224", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. 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Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT4S7", "SAMEA13254180", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254180|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT4S7|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT4S7|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT4S7 s", "Sv2aWT4S7 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT4S7L004-1.fastq.gz", "fastq", 697047881.0, 9227702.0, "E MTAB 11505:sv2aWT4S7L004", "0:75.54 1:0", "A:165881728;C:170388393;G:168105900;T:192572068;N:99792", 75, 0, null, null, 165881728, 170388393, 168105900, 192572068, 99792, "ERX8620335", "ERS10857223", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.9584, null, 0.09565, null, 0.66115, null, 0.46967, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10415, "ERR9077194", "ERX8620334", "ERS10857222", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT3S2", "SAMEA13254179", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT3S2 s", "Sv2aWT3S2 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT3S2L001-1.fastq.gz", "fastq", 723508205.0, 9579193.0, "E MTAB 11505:sv2aWT3S2L001", "0:75.53 1:0", "A:177832489;C:174193135;G:169978598;T:201360184;N:143799", 75, 0, null, null, 177832489, 174193135, 169978598, 201360184, 143799, "ERX8620334", "ERS10857222", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95218, null, 0.11732, null, 0.65916, null, 0.47955, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10416, "ERR9077195", "ERX8620334", "ERS10857222", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT3S2", "SAMEA13254179", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT3S2 s", "Sv2aWT3S2 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT3S2L002-1.fastq.gz", "fastq", 726190024.0, 9614674.0, "E MTAB 11505:sv2aWT3S2L002", "0:75.53 1:0", "A:178408224;C:174776263;G:170820745;T:202047224;N:137568", 75, 0, null, null, 178408224, 174776263, 170820745, 202047224, 137568, "ERX8620334", "ERS10857222", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95093, null, 0.11567, null, 0.65865, null, 0.46877, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10417, "ERR9077196", "ERX8620334", "ERS10857222", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT3S2", "SAMEA13254179", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT3S2 s", "Sv2aWT3S2 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT3S2L003-1.fastq.gz", "fastq", 735499955.0, 9737845.0, "E MTAB 11505:sv2aWT3S2L003", "0:75.53 1:0", "A:180659962;C:177141362;G:172905323;T:204678308;N:115000", 75, 0, null, null, 180659962, 177141362, 172905323, 204678308, 115000, "ERX8620334", "ERS10857222", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95233, null, 0.11614, null, 0.65898, null, 0.47114, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10418, "ERR9077197", "ERX8620334", "ERS10857222", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT3S2", "SAMEA13254179", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254179|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT3S2|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT3S2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT3S2 s", "Sv2aWT3S2 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT3S2L004-1.fastq.gz", "fastq", 745285512.0, 9867337.0, "E MTAB 11505:sv2aWT3S2L004", "0:75.53 1:0", "A:183067487;C:179408382;G:175250814;T:207445912;N:112917", 75, 0, null, null, 183067487, 179408382, 175250814, 207445912, 112917, "ERX8620334", "ERS10857222", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95245, null, 0.11655, null, 0.65857, null, 0.47087, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10419, "ERR9077190", "ERX8620333", "ERS10857221", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT1S1", "SAMEA13254178", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT1S1 s", "Sv2aWT1S1 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT1S1L001-1.fastq.gz", "fastq", 647414748.0, 8571883.0, "E MTAB 11505:sv2aWT1S1L001", "0:75.53 1:0", "A:154593859;C:160498057;G:153809612;T:178389112;N:124108", 75, 0, null, null, 154593859, 160498057, 153809612, 178389112, 124108, "ERX8620333", "ERS10857221", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95955, null, 0.08686, null, 0.65955, null, 0.47406, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10420, "ERR9077191", "ERX8620333", "ERS10857221", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT1S1", "SAMEA13254178", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT1S1 s", "Sv2aWT1S1 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT1S1L002-1.fastq.gz", "fastq", 646657758.0, 8561861.0, "E MTAB 11505:sv2aWT1S1L002", "0:75.53 1:0", "A:154348044;C:160294625;G:153804048;T:178092212;N:118829", 75, 0, null, null, 154348044, 160294625, 153804048, 178092212, 118829, "ERX8620333", "ERS10857221", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95942, null, 0.08632, null, 0.65991, null, 0.47539, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10421, "ERR9077192", "ERX8620333", "ERS10857221", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT1S1", "SAMEA13254178", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT1S1 s", "Sv2aWT1S1 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT1S1L003-1.fastq.gz", "fastq", 654781451.0, 8669333.0, "E MTAB 11505:sv2aWT1S1L003", "0:75.53 1:0", "A:156252744;C:162396721;G:155681450;T:180352911;N:97625", 75, 0, null, null, 156252744, 162396721, 155681450, 180352911, 97625, "ERX8620333", "ERS10857221", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95972, null, 0.08498, null, 0.66137, null, 0.47457, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10422, "ERR9077193", "ERX8620333", "ERS10857221", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aWT1S1", "SAMEA13254178", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254178|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aWT1S1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/+|individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aWT1S1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aWT1S1 s", "Sv2aWT1S1 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/+", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aWT1S1L004-1.fastq.gz", "fastq", 659716937.0, 8734618.0, "E MTAB 11505:sv2aWT1S1L004", "0:75.53 1:0", "A:157367211;C:163585842;G:156911139;T:181757809;N:94936", 75, 0, null, null, 157367211, 163585842, 156911139, 181757809, 94936, "ERX8620333", "ERS10857221", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95985, null, 0.08585, null, 0.65857, null, 0.47349, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10423, "ERR9077186", "ERX8620332", "ERS10857220", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO6S12", "SAMEA13254177", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO6S12 s", "Sv2aHO6S12 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO6S12L001-1.fastq.gz", "fastq", 675018261.0, 8937958.0, "E MTAB 11505:sv2aHO6S12L001", "0:75.52 1:0", "A:166564263;C:160539328;G:160003980;T:187773509;N:137181", 75, 0, null, null, 166564263, 160539328, 160003980, 187773509, 137181, "ERX8620332", "ERS10857220", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94964, null, 0.13009, null, 0.65413, null, 0.47079, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10424, "ERR9077187", "ERX8620332", "ERS10857220", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO6S12", "SAMEA13254177", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO6S12 s", "Sv2aHO6S12 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO6S12L002-1.fastq.gz", "fastq", 672995667.0, 8911161.0, "E MTAB 11505:sv2aHO6S12L002", "0:75.52 1:0", "A:165990319;C:160039398;G:159722501;T:187108781;N:134668", 75, 0, null, null, 165990319, 160039398, 159722501, 187108781, 134668, "ERX8620332", "ERS10857220", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94837, null, 0.13029, null, 0.65744, null, 0.47959, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10425, "ERR9077188", "ERX8620332", "ERS10857220", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO6S12", "SAMEA13254177", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO6S12 s", "Sv2aHO6S12 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO6S12L003-1.fastq.gz", "fastq", 683276767.0, 9047147.0, "E MTAB 11505:sv2aHO6S12L003", "0:75.52 1:0", "A:168501690;C:162583852;G:162063190;T:190018001;N:110034", 75, 0, null, null, 168501690, 162583852, 162063190, 190018001, 110034, "ERX8620332", "ERS10857220", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94983, null, 0.13248, null, 0.6565, null, 0.47977, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10426, "ERR9077189", "ERX8620332", "ERS10857220", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO6S12", "SAMEA13254177", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254177|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO6S12|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO6S12|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO6S12 s", "Sv2aHO6S12 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO6S12L004-1.fastq.gz", "fastq", 686469910.0, 9089431.0, "E MTAB 11505:sv2aHO6S12L004", "0:75.52 1:0", "A:169287189;C:163276361;G:162844724;T:190954218;N:107418", 75, 0, null, null, 169287189, 163276361, 162844724, 190954218, 107418, "ERX8620332", "ERS10857220", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95061, null, 0.13029, null, 0.65389, null, 0.48044, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10427, "ERR9077182", "ERX8620331", "ERS10857219", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO4S10", "SAMEA13254176", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO4S10 s", "Sv2aHO4S10 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO4S10L001-1.fastq.gz", "fastq", 713858966.0, 9452474.0, "E MTAB 11505:sv2aHO4S10L001", "0:75.52 1:0", "A:177913695;C:169425317;G:167540012;T:198835532;N:144410", 75, 0, null, null, 177913695, 169425317, 167540012, 198835532, 144410, "ERX8620331", "ERS10857219", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94848, null, 0.12981, null, 0.6636, null, 0.47772, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10428, "ERR9077183", "ERX8620331", "ERS10857219", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO4S10", "SAMEA13254176", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO4S10 s", "Sv2aHO4S10 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO4S10L002-1.fastq.gz", "fastq", 717619593.0, 9502301.0, "E MTAB 11505:sv2aHO4S10L002", "0:75.52 1:0", "A:178830542;C:170284720;G:168594514;T:199773382;N:136435", 75, 0, null, null, 178830542, 170284720, 168594514, 199773382, 136435, "ERX8620331", "ERS10857219", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94812, null, 0.12868, null, 0.6645, null, 0.47281, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10429, "ERR9077184", "ERX8620331", "ERS10857219", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO4S10", "SAMEA13254176", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO4S10 s", "Sv2aHO4S10 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO4S10L003-1.fastq.gz", "fastq", 727263626.0, 9629858.0, "E MTAB 11505:sv2aHO4S10L003", "0:75.52 1:0", "A:181201278;C:172619520;G:170780953;T:202550397;N:111478", 75, 0, null, null, 181201278, 172619520, 170780953, 202550397, 111478, "ERX8620331", "ERS10857219", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94768, null, 0.12827, null, 0.66596, null, 0.47332, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10430, "ERR9077185", "ERX8620331", "ERS10857219", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO4S10", "SAMEA13254176", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254176|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO4S10|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO4S10|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO4S10 s", "Sv2aHO4S10 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO4S10L004-1.fastq.gz", "fastq", 736595278.0, 9753337.0, "E MTAB 11505:sv2aHO4S10L004", "0:75.52 1:0", "A:183510872;C:174806534;G:173027794;T:205140640;N:109438", 75, 0, null, null, 183510872, 174806534, 173027794, 205140640, 109438, "ERX8620331", "ERS10857219", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94925, null, 0.12904, null, 0.66417, null, 0.47297, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10431, "ERR9077178", "ERX8620330", "ERS10857218", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO3S6", "SAMEA13254175", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO3S6 s", "Sv2aHO3S6 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO3S6L001-1.fastq.gz", "fastq", 710756305.0, 9410862.0, "E MTAB 11505:sv2aHO3S6L001", "0:75.53 1:0", "A:175585613;C:170261120;G:166658917;T:198106388;N:144267", 75, 0, null, null, 175585613, 170261120, 166658917, 198106388, 144267, "ERX8620330", "ERS10857218", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94827, null, 0.14002, null, 0.66785, null, 0.474, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10432, "ERR9077179", "ERX8620330", "ERS10857218", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO3S6", "SAMEA13254175", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO3S6 s", "Sv2aHO3S6 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO3S6L002-1.fastq.gz", "fastq", 715330324.0, 9471415.0, "E MTAB 11505:sv2aHO3S6L002", "0:75.53 1:0", "A:176679775;C:171311031;G:167903237;T:199299483;N:136798", 75, 0, null, null, 176679775, 171311031, 167903237, 199299483, 136798, "ERX8620330", "ERS10857218", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.9469, null, 0.13915, null, 0.67004, null, 0.47654, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10433, "ERR9077180", "ERX8620330", "ERS10857218", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO3S6", "SAMEA13254175", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO3S6 s", "Sv2aHO3S6 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO3S6L003-1.fastq.gz", "fastq", 722810562.0, 9570364.0, "E MTAB 11505:sv2aHO3S6L003", "0:75.53 1:0", "A:178442845;C:173192786;G:169595085;T:201465522;N:114324", 75, 0, null, null, 178442845, 173192786, 169595085, 201465522, 114324, "ERX8620330", "ERS10857218", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94918, null, 0.13979, null, 0.66902, null, 0.47572, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10434, "ERR9077181", "ERX8620330", "ERS10857218", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHO3S6", "SAMEA13254175", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254175|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHO3S6|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a / |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHO3S6|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHO3S6 s", "Sv2aHO3S6 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHO3S6L004-1.fastq.gz", "fastq", 732990507.0, 9705054.0, "E MTAB 11505:sv2aHO3S6L004", "0:75.53 1:0", "A:180951130;C:175567778;G:172037542;T:204323488;N:110569", 75, 0, null, null, 180951130, 175567778, 172037542, 204323488, 110569, "ERX8620330", "ERS10857218", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.94812, null, 0.13893, null, 0.67085, null, 0.47502, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10435, "ERR9077174", "ERX8620329", "ERS10857217", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET7S9", "SAMEA13254174", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET7S9 s", "Sv2aHET7S9 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET7S9L001-1.fastq.gz", "fastq", 773209432.0, 10238087.0, "E MTAB 11505:sv2aHET7S9L001", "0:75.52 1:0", "A:191962953;C:184699376;G:180774008;T:215620759;N:152336", 75, 0, null, null, 191962953, 184699376, 180774008, 215620759, 152336, "ERX8620329", "ERS10857217", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95047, null, 0.12485, null, 0.65705, null, 0.4775, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10436, "ERR9077175", "ERX8620329", "ERS10857217", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET7S9", "SAMEA13254174", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET7S9 s", "Sv2aHET7S9 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET7S9L002-1.fastq.gz", "fastq", 773106152.0, 10236677.0, "E MTAB 11505:sv2aHET7S9L002", "0:75.52 1:0", "A:191812833;C:184676419;G:180997547;T:215473732;N:145621", 75, 0, null, null, 191812833, 184676419, 180997547, 215473732, 145621, "ERX8620329", "ERS10857217", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95016, null, 0.12464, null, 0.65482, null, 0.47419, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10437, "ERR9077176", "ERX8620329", "ERS10857217", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET7S9", "SAMEA13254174", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET7S9 s", "Sv2aHET7S9 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET7S9L003-1.fastq.gz", "fastq", 783061051.0, 10368445.0, "E MTAB 11505:sv2aHET7S9L003", "0:75.52 1:0", "A:194289152;C:187108364;G:183177036;T:218370500;N:115999", 75, 0, null, null, 194289152, 187108364, 183177036, 218370500, 115999, "ERX8620329", "ERS10857217", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95172, null, 0.12488, null, 0.65445, null, 0.48157, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10438, "ERR9077177", "ERX8620329", "ERS10857217", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET7S9", "SAMEA13254174", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254174|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET7S9|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET7S9|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET7S9 s", "Sv2aHET7S9 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET7S9L004-1.fastq.gz", "fastq", 790150025.0, 10462214.0, "E MTAB 11505:sv2aHET7S9L004", "0:75.52 1:0", "A:196056500;C:188746833;G:184927588;T:220305922;N:113182", 75, 0, null, null, 196056500, 188746833, 184927588, 220305922, 113182, "ERX8620329", "ERS10857217", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95285, null, 0.12478, null, 0.65551, null, 0.4763, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10439, "ERR9077170", "ERX8620328", "ERS10857216", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET4S5", "SAMEA13254173", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET4S5 s", "Sv2aHET4S5 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET4S5L001-1.fastq.gz", "fastq", 685650097.0, 9076481.0, "E MTAB 11505:sv2aHET4S5L001", "0:75.54 1:0", "A:161812875;C:167870520;G:166985310;T:188850530;N:130862", 75, 0, null, null, 161812875, 167870520, 166985310, 188850530, 130862, "ERX8620328", "ERS10857216", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95733, null, 0.09974, null, 0.65691, null, 0.47392, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10440, "ERR9077171", "ERX8620328", "ERS10857216", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET4S5", "SAMEA13254173", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET4S5 s", "Sv2aHET4S5 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET4S5L002-1.fastq.gz", "fastq", 684402241.0, 9059974.0, "E MTAB 11505:sv2aHET4S5L002", "0:75.54 1:0", "A:161493428;C:167520248;G:166882054;T:188383816;N:122695", 75, 0, null, null, 161493428, 167520248, 166882054, 188383816, 122695, "ERX8620328", "ERS10857216", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95537, null, 0.09915, null, 0.65719, null, 0.48261, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10441, "ERR9077172", "ERX8620328", "ERS10857216", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET4S5", "SAMEA13254173", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET4S5 s", "Sv2aHET4S5 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET4S5L003-1.fastq.gz", "fastq", 694099126.0, 9188245.0, "E MTAB 11505:sv2aHET4S5L003", "0:75.54 1:0", "A:163727378;C:169989210;G:169143224;T:191137588;N:101726", 75, 0, null, null, 163727378, 169989210, 169143224, 191137588, 101726, "ERX8620328", "ERS10857216", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95629, null, 0.09861, null, 0.65705, null, 0.47187, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10442, "ERR9077173", "ERX8620328", "ERS10857216", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET4S5", "SAMEA13254173", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254173|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET4S5|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET4S5|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET4S5 s", "Sv2aHET4S5 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET4S5L004-1.fastq.gz", "fastq", 698753836.0, 9249820.0, "E MTAB 11505:sv2aHET4S5L004", "0:75.54 1:0", "A:164809473;C:171057633;G:170349692;T:192441413;N:95625", 75, 0, null, null, 164809473, 171057633, 170349692, 192441413, 95625, "ERX8620328", "ERS10857216", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95613, null, 0.09885, null, 0.65798, null, 0.47227, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10443, "ERR9077166", "ERX8620327", "ERS10857215", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET3S4", "SAMEA13254172", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET3S4 s", "Sv2aHET3S4 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET3S4L001-1.fastq.gz", "fastq", 691298605.0, 9151512.0, "E MTAB 11505:sv2aHET3S4L001", "0:75.54 1:0", "A:164743919;C:170752099;G:164763621;T:190912044;N:126922", 75, 0, null, null, 164743919, 170752099, 164763621, 190912044, 126922, "ERX8620327", "ERS10857215", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95684, null, 0.09604, null, 0.6603, null, 0.47285, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10444, "ERR9077167", "ERX8620327", "ERS10857215", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET3S4", "SAMEA13254172", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET3S4 s", "Sv2aHET3S4 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET3S4L002-1.fastq.gz", "fastq", 694080975.0, 9188259.0, "E MTAB 11505:sv2aHET3S4L002", "0:75.54 1:0", "A:165336810;C:171397273;G:165632321;T:191591872;N:122699", 75, 0, null, null, 165336810, 171397273, 165632321, 191591872, 122699, "ERX8620327", "ERS10857215", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95612, null, 0.09694, null, 0.65993, null, 0.46918, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10445, "ERR9077168", "ERX8620327", "ERS10857215", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET3S4", "SAMEA13254172", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET3S4 s", "Sv2aHET3S4 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET3S4L003-1.fastq.gz", "fastq", 703689889.0, 9315387.0, "E MTAB 11505:sv2aHET3S4L003", "0:75.54 1:0", "A:167575230;C:173881977;G:167845574;T:194289403;N:97705", 75, 0, null, null, 167575230, 173881977, 167845574, 194289403, 97705, "ERX8620327", "ERS10857215", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.9577, null, 0.09608, null, 0.66042, null, 0.47022, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10446, "ERR9077169", "ERX8620327", "ERS10857215", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET3S4", "SAMEA13254172", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254172|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET3S4|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET3S4|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET3S4 s", "Sv2aHET3S4 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET3S4L004-1.fastq.gz", "fastq", 712116538.0, 9426961.0, "E MTAB 11505:sv2aHET3S4L004", "0:75.54 1:0", "A:169598596;C:175885948;G:169866534;T:196669400;N:96060", 75, 0, null, null, 169598596, 175885948, 169866534, 196669400, 96060, "ERX8620327", "ERS10857215", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95734, null, 0.09716, null, 0.66054, null, 0.47257, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10447, "ERR9077162", "ERX8620326", "ERS10857214", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET2S3", "SAMEA13254171", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET2S3 s", "Sv2aHET2S3 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET2S3L001-1.fastq.gz", "fastq", 733440522.0, 9709422.0, "E MTAB 11505:sv2aHET2S3L001", "0:75.54 1:0", "A:173670000;C:181175353;G:175392793;T:203059256;N:143120", 75, 0, null, null, 173670000, 181175353, 175392793, 203059256, 143120, "ERX8620326", "ERS10857214", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95885, null, 0.08758, null, 0.65393, null, 0.47249, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10448, "ERR9077163", "ERX8620326", "ERS10857214", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET2S3", "SAMEA13254171", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET2S3 s", "Sv2aHET2S3 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET2S3L002-1.fastq.gz", "fastq", 732121929.0, 9691967.0, "E MTAB 11505:sv2aHET2S3L002", "0:75.54 1:0", "A:173332091;C:180805738;G:175271736;T:202574727;N:137637", 75, 0, null, null, 173332091, 180805738, 175271736, 202574727, 137637, "ERX8620326", "ERS10857214", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95775, null, 0.08879, null, 0.6564, null, 0.4718, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10449, "ERR9077164", "ERX8620326", "ERS10857214", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET2S3", "SAMEA13254171", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET2S3 s", "Sv2aHET2S3 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET2S3L003-1.fastq.gz", "fastq", 743488189.0, 9842286.0, "E MTAB 11505:sv2aHET2S3L003", "0:75.54 1:0", "A:175979238;C:183726319;G:177933958;T:205735955;N:112719", 75, 0, null, null, 175979238, 183726319, 177933958, 205735955, 112719, "ERX8620326", "ERS10857214", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.9593, null, 0.08716, null, 0.65437, null, 0.46976, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [10450, "ERR9077165", "ERX8620326", "ERS10857214", "ERP135966", "PRJEB51339", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E-MTAB-11505", "Transcriptome Analysis", "Transcriptome analysis of the heads of 6 dpf sv2a / sv2a+/ and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a / zebrafish larvae.", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", null, "Protocols: 6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Sv2aHET2S3", "SAMEA13254171", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg", "ENA first public:2022 04 21|ENA last update:2022 04 21|External Id:SAMEA13254171|INSDC center alias:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC center name:Laboratory for Molecular Biodiscovery KU Leuven Campus Gasthuisberg|INSDC first public:2022 04 21T00:32:07Z|INSDC last update:2022 04 21T00:32:07Z|INSDC status:public|Submitter Id:E MTAB 11505:Sv2aHET2S3|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:sv2a+/ |individual:pool of 10 heads|organism part:head|sample name:E MTAB 11505:Sv2aHET2S3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "E MTAB 11505:Sv2aHET2S3 s", "Sv2aHET2S3 s", "RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "6 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled per sample. Total RNA was extracted using TRIzol reagent Invitrogen followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes the RNA pellet was air dried dissolved in nuclease free water Fermentas. TruSeq RNA Seq sample preparation kit was used to prepare sequencing library of mRNA in accordance with the manufacturer guidelines.", "Experimental Factor: genotype:sv2a+/ ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP135966", "NextSeq 500 sequencing; RNA seq experiment of sv2a / sv2a+/ and sv2a+/+ zebrafish larvae", "ENA FIRST PUBLIC:2022 04 21|ENA LAST UPDATE:2022 04 21", "sv2aHET2S3L004-1.fastq.gz", "fastq", 747723481.0, 9898304.0, "E MTAB 11505:sv2aHET2S3L004", "0:75.54 1:0", "A:176935451;C:184684782;G:179046040;T:206946124;N:111084", 75, 0, null, null, 176935451, 184684782, 179046040, 206946124, 111084, "ERX8620326", "ERS10857214", "ERA9644804", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven, Campus Gasthuisberg|European Nucleotide Archive", 1, 0.95934, null, 0.08676, null, 0.65533, null, 0.47523, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-04-21", "Larval", "Larval", "Head", "Nervous System"], [19476, "ERR14208827", "ERX13611047", "ERS22979745", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "Scrambled 1 sample", "SAMEA117628607", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 004|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 004|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: Scrambled 1 sample", "webin reads Scrambled 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: Scrambled 1 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "F04.bam", "bam", 8497741.0, 104283.0, "webin reads Scrambled 1 sample", "0:81.49", "A:2628864;C:1112827;G:2146146;T:2609768;N:136", 81, null, null, null, 2628864, 1112827, 2146146, 2609768, 136, "ERX13611047", "ERS22979745", "ERA31123309", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19477, "ERR14208813", "ERX13611033", "ERS22979748", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "ythdf2KO 1 sample", "SAMEA117628610", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 007|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 007|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 1 sample", "webin reads ythdf2KO 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: ythdf2KO 1 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "D09.bam", "bam", 673213184.0, 8122011.0, "webin reads ythdf2KO 1 sample", "0:82.89", "A:180836688;C:107076381;G:193711319;T:191586188;N:2608", 82, null, null, null, 180836688, 107076381, 193711319, 191586188, 2608, "ERX13611033", "ERS22979748", "ERA31123295", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19478, "ERR14208811", "ERX13611031", "ERS22979755", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "GFP 6 sample", "SAMEA117628617", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 014|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 014|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: GFP 6 sample", "webin reads GFP 6 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: GFP 6 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "H01.bam", "bam", 337553787.0, 3153658.0, "webin reads GFP 6 sample", "0:107.04", "A:81816649;C:55524538;G:113686171;T:86525390;N:1039", 107, null, null, null, 81816649, 55524538, 113686171, 86525390, 1039, "ERX13611031", "ERS22979755", "ERA31123293", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19479, "ERR14208821", "ERX13611041", "ERS22979752", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "ythdf2KO 5 sample", "SAMEA117628614", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 011|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 011|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 5 sample", "webin reads ythdf2KO 5 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: ythdf2KO 5 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "G10.bam", "bam", 226771232.0, 2050630.0, "webin reads ythdf2KO 5 sample", "0:110.59", "A:56944731;C:30766256;G:83820146;T:55239221;N:878", 110, null, null, null, 56944731, 30766256, 83820146, 55239221, 878, "ERX13611041", "ERS22979752", "ERA31123303", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19480, "ERR14208818", "ERX13611038", "ERS22979750", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "ythdf2KO 3 sample", "SAMEA117628612", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 009|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 009|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 3 sample", "webin reads ythdf2KO 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: ythdf2KO 3 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "G08.bam", "bam", 351425328.0, 3771763.0, "webin reads ythdf2KO 3 sample", "0:93.17", "A:83933175;C:50138103;G:128300798;T:89051913;N:1339", 93, null, null, null, 83933175, 50138103, 128300798, 89051913, 1339, "ERX13611038", "ERS22979750", "ERA31123300", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19481, "ERR14208826", "ERX13611046", "ERS22979758", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "YTHDF2 3 sample", "SAMEA117628620", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 017|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 017|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: YTHDF2 3 sample", "webin reads YTHDF2 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: YTHDF2 3 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "E01.bam", "bam", 181017083.0, 1670383.0, "webin reads YTHDF2 3 sample", "0:108.37", "A:38910474;C:31607688;G:67095095;T:43403227;N:599", 108, null, null, null, 38910474, 31607688, 67095095, 43403227, 599, "ERX13611046", "ERS22979758", "ERA31123308", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19482, "ERR14208815", "ERX13611035", "ERS22979749", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "ythdf2KO 2 sample", "SAMEA117628611", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 008|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 008|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 2 sample", "webin reads ythdf2KO 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: ythdf2KO 2 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "D10.bam", "bam", 282414832.0, 2675188.0, "webin reads ythdf2KO 2 sample", "0:105.57", "A:73651155;C:41694223;G:96485766;T:70582706;N:982", 105, null, null, null, 73651155, 41694223, 96485766, 70582706, 982, "ERX13611035", "ERS22979749", "ERA31123297", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19483, "ERR14208804", "ERX13611024", "ERS22979742", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "GFP 1 sample", "SAMEA117628604", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 001|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 001|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: GFP 1 sample", "webin reads GFP 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: GFP 1 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "F01.bam", "bam", 8036009.0, 97716.0, "webin reads GFP 1 sample", "0:82.24", "A:2445867;C:1074319;G:2086526;T:2429153;N:144", 82, null, null, null, 2445867, 1074319, 2086526, 2429153, 144, "ERX13611024", "ERS22979742", "ERA31123286", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19484, "ERR14208829", "ERX13611049", "ERS22979747", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "Scrambled 3 sample", "SAMEA117628609", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 006|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 006|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: Scrambled 3 sample", "webin reads Scrambled 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: Scrambled 3 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "F06.bam", "bam", 90051514.0, 910768.0, "webin reads Scrambled 3 sample", "0:98.87", "A:30132090;C:13700682;G:16323331;T:29894332;N:1079", 98, null, null, null, 30132090, 13700682, 16323331, 29894332, 1079, "ERX13611049", "ERS22979747", "ERA31123311", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19485, "ERR14208809", "ERX13611029", "ERS22979753", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "GFP 4 sample", "SAMEA117628615", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 012|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 012|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: GFP 4 sample", "webin reads GFP 4 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: GFP 4 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "G11.bam", "bam", 72278736.0, 751207.0, "webin reads GFP 4 sample", "0:96.22", "A:17589630;C:11153310;G:25212154;T:18323416;N:226", 96, null, null, null, 17589630, 11153310, 25212154, 18323416, 226, "ERX13611029", "ERS22979753", "ERA31123291", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19486, "ERR14208806", "ERX13611026", "ERS22979743", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "GFP 2 sample", "SAMEA117628605", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 002|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 002|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: GFP 2 sample", "webin reads GFP 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: GFP 2 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "F02.bam", "bam", 19196592.0, 230075.0, "webin reads GFP 2 sample", "0:83.44", "A:5957309;C:2709511;G:4434875;T:6094552;N:345", 83, null, null, null, 5957309, 2709511, 4434875, 6094552, 345, "ERX13611026", "ERS22979743", "ERA31123288", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19487, "ERR14208810", "ERX13611030", "ERS22979754", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "GFP 5 sample", "SAMEA117628616", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 013|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 013|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: GFP 5 sample", "webin reads GFP 5 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: GFP 5 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "G12.bam", "bam", 431708790.0, 5173015.0, "webin reads GFP 5 sample", "0:83.45", "A:119077902;C:68329173;G:126879243;T:117420803;N:1669", 83, null, null, null, 119077902, 68329173, 126879243, 117420803, 1669, "ERX13611030", "ERS22979754", "ERA31123292", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19488, "ERR14208828", "ERX13611048", "ERS22979746", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "Scrambled 2 sample", "SAMEA117628608", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 005|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 005|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: Scrambled 2 sample", "webin reads Scrambled 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: Scrambled 2 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "F05.bam", "bam", 32695808.0, 357320.0, "webin reads Scrambled 2 sample", "0:91.50", "A:10989624;C:4719485;G:5954777;T:11031603;N:319", 91, null, null, null, 10989624, 4719485, 5954777, 11031603, 319, "ERX13611048", "ERS22979746", "ERA31123310", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19489, "ERR14208819", "ERX13611039", "ERS22979751", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "ythdf2KO 4 sample", "SAMEA117628613", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 010|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 010|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: ythdf2KO 4 sample", "webin reads ythdf2KO 4 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: ythdf2KO 4 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "G09.bam", "bam", 254231539.0, 2766205.0, "webin reads ythdf2KO 4 sample", "0:91.91", "A:63984512;C:40328422;G:86431821;T:63485754;N:1030", 91, null, null, null, 63984512, 40328422, 86431821, 63485754, 1030, "ERX13611039", "ERS22979751", "ERA31123301", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19490, "ERR14208808", "ERX13611028", "ERS22979744", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "GFP 3 sample", "SAMEA117628606", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 003|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 003|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: GFP 3 sample", "webin reads GFP 3 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: GFP 3 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "F03.bam", "bam", 35932988.0, 419944.0, "webin reads GFP 3 sample", "0:85.57", "A:11252929;C:5321445;G:8032297;T:11325814;N:503", 85, null, null, null, 11252929, 5321445, 8032297, 11325814, 503, "ERX13611028", "ERS22979744", "ERA31123290", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19491, "ERR14208825", "ERX13611045", "ERS22979757", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "YTHDF2 2 sample", "SAMEA117628619", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 016|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 016|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: YTHDF2 2 sample", "webin reads YTHDF2 2 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: YTHDF2 2 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "D12.bam", "bam", 626993184.0, 7599502.0, "webin reads YTHDF2 2 sample", "0:82.50", "A:182701108;C:91008174;G:172822143;T:180459253;N:2506", 82, null, null, null, 182701108, 91008174, 172822143, 180459253, 2506, "ERX13611045", "ERS22979757", "ERA31123307", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [19492, "ERR14208822", "ERX13611042", "ERS22979756", "ERP167299", "PRJEB83709", "YTHDF2 and ASD DM", "3296f78e-e1c0-43ea-968c-53fe04e67615", "Other", "Among autistic individuals a subphenotype of disproportionate megalencephaly ASD DM seen at three years of age is associated with co occurring intellectual disability and poorer prognoses later in life. However many of the genes contributing to ASD DM have yet to be delineated. In this study we identified additional ASD DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD DM genes harboring de novo protein impacting variants. Our findings include fourteen high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM including CHD8 and PTEN. By performing functional network analysis we expanded to additional candidate genes including one previously implicated in ASD DM PIK3CA as well as 184 additional genes previously implicated in ASD or DM alone. Using zebrafish we modeled a de novo tandem duplication impacting YTHDF2 encoding an N6 methyladenosine m6A mRNA reader in an ASD DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size while overexpressing YTHDF2 resulted in increased head and brain size matching that of the proband. Single cell transcriptomes of YTHDF2 gain of function larvae point to reduced expression of Fragile X syndrome associated FMRP target genes globally and in the developing brain providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader YTHDC1 in our ASD DM cohort. Though we highlight only two cases to date our study provides support for the m6A RNA modification pathway as potentially contributing to this severe form of autism.", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", null, "Single cell RNA sequencing of zebrafish heads", "YTHDF2 1 sample", "SAMEA117628618", "UNIVERSITY OF CALIFORNIA - DAVIS", "ENA first public:2025 02 01|INSDC center name:UNIVERSITY OF CALIFORNIA DAVIS|INSDC status:public|Submitter Id:Sample 015|collection date:2022 08 07|common name:zebrafish|dev stage:72 hpf|geographic location country and/or sea:USA|sample name:Sample 015|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Raw reads: YTHDF2 1 sample", "webin reads YTHDF2 1 sample", null, "unspecified", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP167299", "Raw reads: YTHDF2 1 sample", "ENA FIRST PUBLIC:2025 02 01|ENA LAST UPDATE:2025 02 01", "D11.bam", "bam", 120748751.0, 1368887.0, "webin reads YTHDF2 1 sample", "0:88.21", "A:34957526;C:19985010;G:32927086;T:32878659;N:470", 88, null, null, null, 34957526, 19985010, 32927086, 32878659, 470, "ERX13611042", "ERS22979756", "ERA31123304", "UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive", "UNIVERSITY OF CALIFORNIA - DAVIS", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-02-01", "Larval", "Larval", "Head", "Nervous System"], [32037, "SRR28992909", "SRX24520261", "SRS21267950", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Wt1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Wt1", "Kcnd2 Wt1", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Kcnd2_Wt1.fq.gz", "fastq", 3386455050.0, 22576367.0, "Kcnd2 Wt1.fq.gz", "0:150", "A:967137430;C:730108913;G:738646978;T:950549427;N:12302", 150, null, null, null, 967137430, 730108913, 738646978, 950549427, 12302, "SRX24520261", "SRS21267950", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [32038, "SRR28992910", "SRX24520260", "SRS21267949", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Hom3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Hom3", "Arfgef1 Hom3", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Arfgef1_Hom3.fq.gz", "fastq", 3647365500.0, 24315770.0, "Arfgef1 Hom3.fq.gz", "0:150", "A:923919033;C:903440333;G:911845870;T:908147370;N:12894", 150, null, null, null, 923919033, 903440333, 911845870, 908147370, 12894, "SRX24520260", "SRS21267949", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [32039, "SRR28992915", "SRX24520258", "SRS21267947", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Hom1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Hom1", "Arfgef1 Hom1", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Arfgef1_Hom1.fq.gz", "fastq", 3388869300.0, 22592462.0, "Arfgef1 Hom1.fq.gz", "0:150", "A:869162615;C:827706442;G:835453288;T:856534517;N:12438", 150, null, null, null, 869162615, 827706442, 835453288, 856534517, 12438, "SRX24520258", "SRS21267947", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [32040, "SRR28992912", "SRX24520257", "SRS21267946", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Het3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Het3", "Arfgef1 Het3", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Arfgef1_Het3.fq.gz", "fastq", 3369996750.0, 22466645.0, "Arfgef1 Het3.fq.gz", "0:150", "A:861941573;C:824864964;G:833793356;T:849388791;N:8066", 150, null, null, null, 861941573, 824864964, 833793356, 849388791, 8066, "SRX24520257", "SRS21267946", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [32041, "SRR28992913", "SRX24520256", "SRS21267945", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Het2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Het2", "Arfgef1 Het2", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Arfgef1_Het2.fq.gz", "fastq", 4755406500.0, 31702710.0, "Arfgef1 Het2.fq.gz", "0:150", "A:1254995507;C:1127923454;G:1138127034;T:1234180808;N:179697", 150, null, null, null, 1254995507, 1127923454, 1138127034, 1234180808, 179697, "SRX24520256", "SRS21267945", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [32042, "SRR28992916", "SRX24520254", "SRS21267943", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Hom3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Hom3", "Wnt8b Hom3", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Wnt8b_Hom3.fq.gz", "fastq", 5283928950.0, 35226193.0, "Wnt8b Hom3.fq.gz", "0:150", "A:1389228037;C:1262004726;G:1265392219;T:1367105548;N:198420", 150, null, null, null, 1389228037, 1262004726, 1265392219, 1367105548, 198420, "SRX24520254", "SRS21267943", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [32043, "SRR28992919", "SRX24520251", "SRS21267940", "SRP506997", "PRJNA1110229", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1110229", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes of which 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore RNAseq revealed convergent transcriptional abnormalities between mutant lines consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1 KCND2 and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Het3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Het3", "Wnt8b Het3", "Three replicate larvae from Het in crosses aged 5 dpf were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506997", null, null, "Wnt8b_Het3.fq.gz", "fastq", 4357330950.0, 29048873.0, "Wnt8b Het3.fq.gz", "0:150", "A:1179652667;C:1002955689;G:1008147493;T:1166494534;N:80567", 150, null, null, null, 1179652667, 1002955689, 1008147493, 1166494534, 80567, "SRX24520251", "SRS21267940", "SRA1863814", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-10", "Larval", "Larval", "Head", "Nervous System"], [36479, "SRR527834", "SRX171221", "SRS352107", "SRP014596", "PRJNA171539", "Transcriptomic analysis of zebrafish during development and homeostasis", "GSE39703", "Transcriptome Analysis", "Sequencing libraries were generated from total RNA samples following the mRNAseq protocol for the generation of single end 16 hpf 36 hpf 5 day larvae adult head and adult tail or paired end 24 hpf libraries Illumina. Single end reads of 36 nucleotides and paired end reads 2 x 76 nucleotides were obtained with a GAIIx Illumina. Gene expression at the different stages/tissu was assessed by cufflinks and HTseq. Overall design: RNAseq on 5 differents samples: 24hpf embryos pool of 16 hour to 36 hour embryos 5 dpf larvea adult head and adult tail", null, "pubmed:23684812", null, "head", "GSM977959", null, "tissue:entire adult head|genotype:Wild type|strain:AB|Stage:adult head", "head", "Basecalls performed using CASAVA version 1.4 Reads aligned to zebrafish genome Zv9 Ensembl with Tophat v 1.4.1 and Bowtie v 0.12.7 options: butterfly search coverage search microexon search min anchor length 5 G GTF Determination of raw reads aligned to ZV9 with HTSeq v0.5.3p3 and gtf file ensembl zv9 release 60 Determination of RPKM/FPKM with cufflinks v 1.3.0 with the options u b M rRNA/Mtgenes mask G gtf Genome build: Zv9 v 60 Supplementary files format and content: *.count file are the output of Htseq reads quantification. *.fpkm files are the output of cufflinks quantification", "entire adult head", null, "Extraction of total RNA with Trizol following manufacturer's instruction. Generation of mRNA libraries with Trueseq RNA kit following Illumina's instructions", null, "genotype:Wild type|strain:AB|Stage:adult head", "GSM977959", "GSM977959: head; Danio rerio; RNA Seq", "GSM977959 1", "GSM977959: head", "1", null, "GEO Accession:GSM977959", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "360Application ReadForward1", "SRP014596", null, null, null, null, 516054600.0, 14334850.0, "GSM977959 r1", "0:36", "A:144148482;C:115800670;G:121205261;T:134746787;N:153400", 36, null, null, null, 144148482, 115800670, 121205261, 134746787, 153400, "SRX171221", "SRS352107", "SRA056408", "GEO", "ITG", 1, 0.89668, null, 0.12577, null, 0.66803, null, 0.45871, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2012-07-27", "Adult", "Adult", "Head", "Nervous System"], [39887, "SRR2239197", "SRX1181673", "SRS1053962", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "mutant 5 hr treatment replicate 3", "GSM1868446", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head", "mutant 5 hr treatment replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head", "GSM1868446", "GSM1868446: mutant 5 hr treatment replicate 3; Danio rerio; RNA Seq", "GSM1868446", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868446", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1349_s_3_withindex_sequence.txt_AGGCGAA.fq.gz", "fastq", 1486758800.0, 29735176.0, "GSM1868446 r1", "0:50", "A:407157206;C:348516474;G:333581236;T:397373823;N:130061", 50, null, null, null, 407157206, 348516474, 333581236, 397373823, 130061, "SRX1181673", "SRS1053962", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89356, null, 0.24716, null, 0.66348, null, 0.55072, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39888, "SRR2239196", "SRX1181672", "SRS1053963", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "mutant 5 hr treatment replicate 2", "GSM1868445", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head", "mutant 5 hr treatment replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head", "GSM1868445", "GSM1868445: mutant 5 hr treatment replicate 2; Danio rerio; RNA Seq", "GSM1868445", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868445", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1349_s_3_withindex_sequence.txt_AATTCAT.fq.gz", "fastq", 1324305100.0, 26486102.0, "GSM1868445 r1", "0:50", "A:346866338;C:322967018;G:303987755;T:350367920;N:116069", 50, null, null, null, 346866338, 322967018, 303987755, 350367920, 116069, "SRX1181672", "SRS1053963", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.86992, null, 0.2794, null, 0.67087, null, 0.45, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39889, "SRR2239195", "SRX1181671", "SRS1053965", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "mutant 5 hr treatment replicate 1", "GSM1868444", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head", "mutant 5 hr treatment replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:metronidazole|time:5 hr|tissue:head", "GSM1868444", "GSM1868444: mutant 5 hr treatment replicate 1; Danio rerio; RNA Seq", "GSM1868444", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868444", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1349_s_3_withindex_sequence.txt_CTGCAAT.fq.gz", "fastq", 1996223000.0, 39924460.0, "GSM1868444 r1", "0:50", "A:548376523;C:462971670;G:439194387;T:545504649;N:175771", 50, null, null, null, 548376523, 462971670, 439194387, 545504649, 175771, "SRX1181671", "SRS1053965", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.90072, null, 0.27661, null, 0.66809, null, 0.54999, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39890, "SRR2239194", "SRX1181670", "SRS1053966", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "mutant control replicate 3", "GSM1868443", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head", "mutant control replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head", "GSM1868443", "GSM1868443: mutant control replicate 3; Danio rerio; RNA Seq", "GSM1868443", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868443", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1349_s_3_withindex_sequence.txt_GTAAAAA.fq.gz", "fastq", 1689695100.0, 33793902.0, "GSM1868443 r1", "0:50", "A:469281850;C:387188418;G:368970934;T:464103273;N:150625", 50, null, null, null, 469281850, 387188418, 368970934, 464103273, 150625, "SRX1181670", "SRS1053966", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.88353, null, 0.30543, null, 0.66785, null, 0.53952, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39891, "SRR2239193", "SRX1181669", "SRS1053964", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "mutant control replicate 2", "GSM1868442", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head", "mutant control replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head", "GSM1868442", "GSM1868442: mutant control replicate 2; Danio rerio; RNA Seq", "GSM1868442", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868442", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1349_s_3_withindex_sequence.txt_TGGCATA.fq.gz", "fastq", 1744754500.0, 34895090.0, "GSM1868442 r1", "0:50", "A:475432211;C:407457752;G:387941759;T:473768506;N:154272", 50, null, null, null, 475432211, 407457752, 387941759, 473768506, 154272, "SRX1181669", "SRS1053964", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.8967, null, 0.27571, null, 0.66342, null, 0.5413, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39892, "SRR2239192", "SRX1181668", "SRS1053967", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "mutant control replicate 1", "GSM1868441", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head", "mutant control replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:foxd3 / |agent:control|tissue:head", "GSM1868441", "GSM1868441: mutant control replicate 1; Danio rerio; RNA Seq", "GSM1868441", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868441", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1349_s_3_withindex_sequence.txt_GGAGTCC.fq.gz", "fastq", 1300091300.0, 26001826.0, "GSM1868441 r1", "0:50", "A:356312292;C:301731841;G:287159447;T:354773803;N:113917", 50, null, null, null, 356312292, 301731841, 287159447, 354773803, 113917, "SRX1181668", "SRS1053967", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89407, null, 0.27485, null, 0.66263, null, 0.54402, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39893, "SRR2239190", "SRX1181667", "SRS1053968", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 3", "GSM1868440", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868440", "GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq", "GSM1868440", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_GGTCCTC.fq.gz", "fastq", 788127550.0, 15762551.0, "GSM1868440 r1", "0:50", "A:219123307;C:174342061;G:168810140;T:225814483;N:37559", 50, null, null, null, 219123307, 174342061, 168810140, 225814483, 37559, "SRX1181667", "SRS1053968", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89391, null, 0.27826, null, 0.67034, null, 0.55775, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39894, "SRR2239191", "SRX1181667", "SRS1053968", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 3", "GSM1868440", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868440", "GSM1868440: wild type 5 hr treatment replicate 3; Danio rerio; RNA Seq", "GSM1868440", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_GGTCCTC.fq.gz", "fastq", 779058950.0, 15581179.0, "GSM1868440 r2", "0:50", "A:216843690;C:172197112;G:166801096;T:223172377;N:44675", 50, null, null, null, 216843690, 172197112, 166801096, 223172377, 44675, "SRX1181667", "SRS1053968", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89268, null, 0.27974, null, 0.67067, null, 0.55617, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39895, "SRR2239188", "SRX1181666", "SRS1053969", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 2", "GSM1868439", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868439", "GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq", "GSM1868439", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_GCTTAGA.fq.gz", "fastq", 884810450.0, 17696209.0, "GSM1868439 r1", "0:50", "A:244801024;C:196884736;G:189692109;T:253390454;N:42127", 50, null, null, null, 244801024, 196884736, 189692109, 253390454, 42127, "SRX1181666", "SRS1053969", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89625, null, 0.26571, null, 0.66247, null, 0.52896, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39896, "SRR2239189", "SRX1181666", "SRS1053969", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 2", "GSM1868439", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868439", "GSM1868439: wild type 5 hr treatment replicate 2; Danio rerio; RNA Seq", "GSM1868439", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_GCTTAGA.fq.gz", "fastq", 875476350.0, 17509527.0, "GSM1868439 r2", "0:50", "A:242411986;C:194719083;G:187698234;T:250595738;N:51309", 50, null, null, null, 242411986, 194719083, 187698234, 250595738, 51309, "SRX1181666", "SRS1053969", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89632, null, 0.26574, null, 0.66332, null, 0.53633, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39897, "SRR2239186", "SRX1181665", "SRS1053970", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 1", "GSM1868438", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868438", "GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq", "GSM1868438", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868438", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_GTCGATA.fq.gz", "fastq", 981479900.0, 19629598.0, "GSM1868438 r1", "0:50", "A:272447863;C:217586061;G:210457740;T:280941539;N:46697", 50, null, null, null, 272447863, 217586061, 210457740, 280941539, 46697, "SRX1181665", "SRS1053970", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89259, null, 0.28519, null, 0.66413, null, 0.54434, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39898, "SRR2239187", "SRX1181665", "SRS1053970", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 5 hr treatment replicate 1", "GSM1868438", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "wild type 5 hr treatment replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:5 hr|tissue:head", "GSM1868438", "GSM1868438: wild type 5 hr treatment replicate 1; Danio rerio; RNA Seq", "GSM1868438", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868438", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_GTCGATA.fq.gz", "fastq", 970627300.0, 19412546.0, "GSM1868438 r2", "0:50", "A:269587370;C:215107358;G:208077535;T:277799059;N:55978", 50, null, null, null, 269587370, 215107358, 208077535, 277799059, 55978, "SRX1181665", "SRS1053970", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.8924, null, 0.2863, null, 0.66486, null, 0.54277, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39899, "SRR2239184", "SRX1181664", "SRS1053971", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 2 hr treatment replicate 3", "GSM1868437", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "wild type 2 hr treatment replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "GSM1868437", "GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq", "GSM1868437", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868437", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_AGATACT.fq.gz", "fastq", 1034107450.0, 20682149.0, "GSM1868437 r1", "0:50", "A:263807622;C:250451504;G:242163638;T:277636652;N:48034", 50, null, null, null, 263807622, 250451504, 242163638, 277636652, 48034, "SRX1181664", "SRS1053971", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.90878, null, 0.23218, null, 0.65916, null, 0.49411, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39900, "SRR2239185", "SRX1181664", "SRS1053971", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 2 hr treatment replicate 3", "GSM1868437", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "wild type 2 hr treatment replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "GSM1868437", "GSM1868437: wild type 2 hr treatment replicate 3; Danio rerio; RNA Seq", "GSM1868437", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868437", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_AGATACT.fq.gz", "fastq", 1021705150.0, 20434103.0, "GSM1868437 r2", "0:50", "A:260838269;C:247381617;G:239188036;T:274238961;N:58267", 50, null, null, null, 260838269, 247381617, 239188036, 274238961, 58267, "SRX1181664", "SRS1053971", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.91116, null, 0.23255, null, 0.65918, null, 0.49596, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39901, "SRR2239182", "SRX1181663", "SRS1053972", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 2 hr treatment replicate 2", "GSM1868436", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "wild type 2 hr treatment replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "GSM1868436", "GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq", "GSM1868436", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868436", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_GGGTCAA.fq.gz", "fastq", 756008650.0, 15120173.0, "GSM1868436 r1", "0:50", "A:209261412;C:168123618;G:163450516;T:215134424;N:38680", 50, null, null, null, 209261412, 168123618, 163450516, 215134424, 38680, "SRX1181663", "SRS1053972", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.8978, null, 0.26699, null, 0.66172, null, 0.53653, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39902, "SRR2239183", "SRX1181663", "SRS1053972", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 2 hr treatment replicate 2", "GSM1868436", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "wild type 2 hr treatment replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "GSM1868436", "GSM1868436: wild type 2 hr treatment replicate 2; Danio rerio; RNA Seq", "GSM1868436", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868436", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_GGGTCAA.fq.gz", "fastq", 747959000.0, 14959180.0, "GSM1868436 r2", "0:50", "A:207110574;C:166254650;G:161670187;T:212878047;N:45542", 50, null, null, null, 207110574, 166254650, 161670187, 212878047, 45542, "SRX1181663", "SRS1053972", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89508, null, 0.26657, null, 0.66373, null, 0.53734, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39903, "SRR2239180", "SRX1181662", "SRS1053973", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 2 hr treatment replicate 1", "GSM1868435", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "wild type 2 hr treatment replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "GSM1868435", "GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq", "GSM1868435", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_CAATATC.fq.gz", "fastq", 843938700.0, 16878774.0, "GSM1868435 r1", "0:50", "A:235353785;C:185755129;G:180220044;T:242567413;N:42329", 50, null, null, null, 235353785, 185755129, 180220044, 242567413, 42329, "SRX1181662", "SRS1053973", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.8819, null, 0.31587, null, 0.6719, null, 0.53852, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39904, "SRR2239181", "SRX1181662", "SRS1053973", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type 2 hr treatment replicate 1", "GSM1868435", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "wild type 2 hr treatment replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:metronidazole|time:2 hr|tissue:head", "GSM1868435", "GSM1868435: wild type 2 hr treatment replicate 1; Danio rerio; RNA Seq", "GSM1868435", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_CAATATC.fq.gz", "fastq", 837375500.0, 16747510.0, "GSM1868435 r2", "0:50", "A:233691274;C:184249473;G:178762050;T:240622009;N:50694", 50, null, null, null, 233691274, 184249473, 178762050, 240622009, 50694, "SRX1181662", "SRS1053973", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.88228, null, 0.31306, null, 0.67042, null, 0.53933, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39905, "SRR2239178", "SRX1181661", "SRS1053976", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type control replicate 3", "GSM1868434", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "wild type control replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "GSM1868434", "GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq", "GSM1868434", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_ACCCACT.fq.gz", "fastq", 946427500.0, 18928550.0, "GSM1868434 r1", "0:50", "A:260851494;C:211313068;G:205344403;T:268874280;N:44255", 50, null, null, null, 260851494, 211313068, 205344403, 268874280, 44255, "SRX1181661", "SRS1053976", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89626, null, 0.27082, null, 0.66058, null, 0.53343, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39906, "SRR2239179", "SRX1181661", "SRS1053976", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type control replicate 3", "GSM1868434", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "wild type control replicate 3", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "GSM1868434", "GSM1868434: wild type control replicate 3; Danio rerio; RNA Seq", "GSM1868434", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_ACCCACT.fq.gz", "fastq", 935318450.0, 18706369.0, "GSM1868434 r2", "0:50", "A:258004973;C:208706255;G:202911059;T:265642847;N:53316", 50, null, null, null, 258004973, 208706255, 202911059, 265642847, 53316, "SRX1181661", "SRS1053976", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89576, null, 0.27216, null, 0.663, null, 0.53587, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39907, "SRR2239176", "SRX1181660", "SRS1053974", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type control replicate 2", "GSM1868433", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "wild type control replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "GSM1868433", "GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq", "GSM1868433", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_TCAACTG.fq.gz", "fastq", 914021500.0, 18280430.0, "GSM1868433 r1", "0:50", "A:252009242;C:204125475;G:197760562;T:260083313;N:42908", 50, null, null, null, 252009242, 204125475, 197760562, 260083313, 42908, "SRX1181660", "SRS1053974", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89646, null, 0.26998, null, 0.65979, null, 0.53202, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39908, "SRR2239177", "SRX1181660", "SRS1053974", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type control replicate 2", "GSM1868433", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "wild type control replicate 2", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "GSM1868433", "GSM1868433: wild type control replicate 2; Danio rerio; RNA Seq", "GSM1868433", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_TCAACTG.fq.gz", "fastq", 904836300.0, 18096726.0, "GSM1868433 r2", "0:50", "A:249726925;C:201939252;G:195727802;T:257389594;N:52727", 50, null, null, null, 249726925, 201939252, 195727802, 257389594, 52727, "SRX1181660", "SRS1053974", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89504, null, 0.27105, null, 0.6607, null, 0.5314, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39909, "SRR2239174", "SRX1181659", "SRS1053975", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type control replicate 1", "GSM1868432", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "wild type control replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "GSM1868432", "GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq", "GSM1868432", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_6_withindex_sequence.txt_TTTAACT.fq.gz", "fastq", 919147800.0, 18382956.0, "GSM1868432 r1", "0:50", "A:255238211;C:203629686;G:197780664;T:262454873;N:44366", 50, null, null, null, 255238211, 203629686, 197780664, 262454873, 44366, "SRX1181659", "SRS1053975", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89498, null, 0.2793, null, 0.6636, null, 0.54563, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [39910, "SRR2239175", "SRX1181659", "SRS1053975", "SRP063290", "PRJNA294660", "Transcriptome analysis of metronidazole induced sensory neuron ablation in zebrafish", "GSE72682", "Transcriptome Analysis", "Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells] with the result that very little is known regarding how the non myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap given that over 80% of cutaneous fibers are unmyelinated that they transduce such important modalities as itch pain temperature touch and pressure and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non myelinating glia roles to nerve degeneration. We utilized RNA seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild type larvae and in larvae that do not have peripheral glia foxd3 mutants using a selective conditional approach. Overall the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage. Overall design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild type: control 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.", null, "pubmed:26863206", null, "wild type control replicate 1", "GSM1868432", null, "source name:head|age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "wild type control replicate 1", "Read alignment used STAR ver 2.0.04b Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads total number of uniquely aligned reads genes and transcripts detected ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3. All gene level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold changes FC > 1.2 together with false discovery rate FDR adjusted p values less than or equal to 0.05. R/Bioconductor package \u201cgplots\u201d was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system http://pantherdb.org/genes/index.jsp then GO enrichment analysis was performed in ToppGene suite with the p value cut off < 0.05 B&H corrected. Genome build: Danio rerio Zv9 assembly from Ensembl Supplementary files format and content: wt.txt and mutant.txt report gene counts RPKMs", "head", "For treated samples 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", null, "age:4 dpf|developmental stage:larvae|genotype/variation:AB wild type|agent:control|tissue:head", "GSM1868432", "GSM1868432: wild type control replicate 1; Danio rerio; RNA Seq", "GSM1868432", null, "1", "Heads of 4 dpf larvae exposed to 10 mM MET for either 0 2 or 5 hours were dissected using a small scalpel with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol Life Technologies and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit Qiagen Inc.. Biological triplicates 8 heads per replicate were prepared for each condition. RNA purity and integrity was determined using an Agilent Bioanalyzer 2100 and only those samples having a RIN > 8.7 were used. For library construction 1 \u03bcg total RNA was used for each wild type replicate and 0.35 \u03bcg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo Zero protocol Epicentre. cDNA was synthesized blunt ended an A base added to the 3\u2019 ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.", "GEO Accession:GSM1868432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP063290", null, null, "run_1266_s_7_withindex_sequence.txt_TTTAACT.fq.gz", "fastq", 908786950.0, 18175739.0, "GSM1868432 r2", "0:50", "A:252518589;C:201251252;G:195514386;T:259449857;N:52866", 50, null, null, null, 252518589, 201251252, 195514386, 259449857, 52866, "SRX1181659", "SRS1053975", "SRA294351", "GEO", "Voigt, Pharmacology and Physiology, Saint Louis University", 1, 0.89351, null, 0.27857, null, 0.66492, null, 0.54418, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2015-09-03", "Larval", "Larval", "Head", "Nervous System"], [41655, "SRR5115728", "SRX2431099", "SRS1866976", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "18 hpi rep5", "GSM2430667", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "18 hpi rep5", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "GSM2430667", "GSM2430667: 18 hpi rep5; Danio rerio; RNA Seq", "GSM2430667", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430667", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "18hpi_54366.fastq.gz", "fastq", 3043532908.0, 58529479.0, "GSM2430667 r1", "0:52", "A:729034781;C:769509924;G:743085356;T:801831768;N:71079", 52, null, null, null, 729034781, 769509924, 743085356, 801831768, 71079, "SRX2431099", "SRS1866976", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.73906, null, 0.22225, null, 0.74061, null, 0.49988, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"], [41656, "SRR5115727", "SRX2431098", "SRS1866975", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "18 hpi rep4", "GSM2430666", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "18 hpi rep4", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "GSM2430666", "GSM2430666: 18 hpi rep4; Danio rerio; RNA Seq", "GSM2430666", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430666", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "18hpi_48592.fastq.gz", "fastq", 2622132240.0, 50425620.0, "GSM2430666 r1", "0:52", "A:566371236;C:777180578;G:659521124;T:618999154;N:60148", 52, null, null, null, 566371236, 777180578, 659521124, 618999154, 60148, "SRX2431098", "SRS1866975", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.92057, null, 0.28475, null, 0.86833, null, 0.72823, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"], [41657, "SRR5115726", "SRX2431097", "SRS1866974", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "18 hpi rep3", "GSM2430665", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "18 hpi rep3", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "GSM2430665", "GSM2430665: 18 hpi rep3; Danio rerio; RNA Seq", "GSM2430665", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430665", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "18hpi_48591.fastq.gz", "fastq", 2478119176.0, 47656138.0, "GSM2430665 r1", "0:52", "A:493736890;C:768557459;G:661870968;T:553896608;N:57251", 52, null, null, null, 493736890, 768557459, 661870968, 553896608, 57251, "SRX2431097", "SRS1866974", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.96537, null, 0.26164, null, 0.87892, null, 0.7204, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"], [41658, "SRR5115725", "SRX2431096", "SRS1866973", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "18 hpi rep2", "GSM2430664", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "18 hpi rep2", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "GSM2430664", "GSM2430664: 18 hpi rep2; Danio rerio; RNA Seq", "GSM2430664", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430664", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "18hpi_48590.fastq.gz", "fastq", 2414695452.0, 46436451.0, "GSM2430664 r1", "0:52", "A:475090050;C:755838280;G:657771658;T:525939134;N:56330", 52, null, null, null, 475090050, 755838280, 657771658, 525939134, 56330, "SRX2431096", "SRS1866973", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.9654, null, 0.26982, null, 0.89676, null, 0.72161, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"], [41659, "SRR5115724", "SRX2431095", "SRS1866972", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "18 hpi rep1", "GSM2430663", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "18 hpi rep1", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:18", "GSM2430663", "GSM2430663: 18 hpi rep1; Danio rerio; RNA Seq", "GSM2430663", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430663", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "18hpi_48589.fastq.gz", "fastq", 2275983060.0, 43768905.0, "GSM2430663 r1", "0:52", "A:466133336;C:694614756;G:598071579;T:517110546;N:52843", 52, null, null, null, 466133336, 694614756, 598071579, 517110546, 52843, "SRX2431095", "SRS1866972", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.94909, null, 0.2695, null, 0.86809, null, 0.70019, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"], [41660, "SRR5115723", "SRX2431094", "SRS1866971", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "9 hpi rep5", "GSM2430662", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9", "9 hpi rep5", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9", "GSM2430662", "GSM2430662: 9 hpi rep5; Danio rerio; RNA Seq", "GSM2430662", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430662", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "9hpi_54368.fastq.gz", "fastq", 2831111348.0, 54444449.0, "GSM2430662 r1", "0:52", "A:674270099;C:713818041;G:694997603;T:747958840;N:66765", 52, null, null, null, 674270099, 713818041, 694997603, 747958840, 66765, "SRX2431094", "SRS1866971", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.81449, null, 0.24117, null, 0.74091, null, 0.53961, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"], [41661, "SRR5115722", "SRX2431093", "SRS1866970", "SRP095238", "PRJNA357683", "Transcriptome and Functional Analyses Reveal Roles For Regulators of Epigenetic States Micro RNA Processing And Long Non Coding RNA In Myocyte Dedifferentiation: Insights Into Reprogramming A \u201cPost Mitotic\u201d Cell", "GSE92489", "Transcriptome Analysis", "Purpose: The ability of adult zebrafish tissues to undergo dedifferentiation provides an opportunity to probe the molecular underpinnings of cell identity and reprogramming. Zebafish muscle regeneration utilizes dedifferentiation to reprogram mature multinucleated myocytes into dedifferentiated myoblast that re enter the cell cycle. A unique advantage of this system is that the regenerating cell mass is large and fairly homogenous facilitating genomics approaches to uncovering the underlying biology. Methods: To better understand cellular reprogramming of mature myocytes we temporally analyzed the changing transcriptome leading up to the proliferative switch. RNA was obtained post Laser Micro dissection LMD of Control 9 xxx post injury HPI or 18 HPI using Trizol and micro column purification. Illumina''s TruSeq Stranded mRNA Library Prep Kit and 0.1 4 \u00b5g total mRNA from pooled purified RNA samples were used for performing ribosomal depletion Ribo Zero Gold rRNA Removal Kit Illumina and library preparation. Sequencing was performed by the UM DNA Sequencing Core using an Illumina Hi Seq 2000 50 cycle single end read platform. Results: Clustering and functional annotation of differentially expressed genes highlighted the importance of catabolic and phagocytic processes upregulation at 9 and 18 xxx post injury hpi. Furthermore genes encoding principle regulators of chromatin states were actively re regulated during the reprogramming process. Utilizing the accessibility of these tissues in the zebrafish model kKnockdown experiments enabled in vivo validation and phenotypic analysis of candidate genes and pathways for their roles in genomic and cellular reprogramming. Additionally we found that despite of their low expression levels lncRNAs were highly represented in gene clusters with dynamic \u201cswitch like\u201d expression profiles and that miRNA processing was also found important for reprogramming Conclusions: We conclude that reprogramming of a \u201cpost mitotic\u201d myocyte into a dedifferentiated myoblast requires both heritable yet nuanced epigenetic alterations and molecular switches that involve transcription factors miRNA and lncRNA while maintaining the lineage restriction of the cell of origin. Overall design: Early time xxx post injury 9 & 18 hours mRNA and lncRNA profiles of Zebrafish lateral eye muscle EOM were generated by deep sequencing in quadruplicate using Illumina Hi seq.", null, "pubmed:29121865", null, "9 hpi rep4", "GSM2430661", null, "source name:lateral rectus EOM|genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9", "9 hpi rep4", "We checked the quality of the raw reads data for each sample using FastQC version 0.11.3 to identify features of the data that may indicate quality problems e.g. low quality scores over represented sequences inappropriate GC content etc.. We used the software package Tuxedo Suite for alignment differential expression analysis and post analysis diagnostics. We aligned reads to the reference genome followed by the transcriptome GRCz10 using TopHat version 2.0.13 and Bowtie version 2.2.1. We used default parameter settings for alignment with the exception of: \u201c b2 very sensitive\u201d telling the software to spend extra time searching for valid alignments and \u201c max intron length\u201d of 400 kbs. Novel transcript discovery was not performed employing \u201c no coverage search\u201d and \u201c no novel juncs\u201d to limit the read mapping to known transcripts. We used Cufflinks/CuffDiff version 2.2.1 for expression quantitation and differential expression analysis using NCBI GRCz10.fa as the reference genome sequence and NCBI GRCz10.gtf as the reference transcriptome annotation. For this analysis we used parameter settings: \u201c multi read correct\u201d to adjust expression calculations for reads that map in more than one locus as well as \u201c compatible hits norm\u201d and \u201c upper quartile \u2013norm\u201d for normalization of expression values. We generated diagnostic plots using the CummeRbund package. Genome build: GRCz10 Supplementary files format and content: Processed Data Files include annotated fold change tab delimited files and differential expression tab delimited files", "lateral rectus EOM", null, "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype:actin:GFP|tissue:lateral rectus EOM|xxx post injury:9", "GSM2430661", "GSM2430661: 9 hpi rep4; Danio rerio; RNA Seq", "GSM2430661", null, "1", "Fish heads were were removed decalcified in ammonium sulfate EDTA mixture frozen cryosectioned and lateral rectus isolated by LMD. RNA was harvested using Trizol reagent followed by Reliaprep tissue Miniprep system. Illumina TruSeq Stranded mRNA Library Prep Kit and 0.1 to 4 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2430661", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095238", null, null, "9hpi_48586.fastq.gz", "fastq", 3247890880.0, 62459440.0, "GSM2430661 r1", "0:52", "A:737775958;C:866361850;G:806031275;T:837644754;N:77043", 52, null, null, null, 737775958, 866361850, 806031275, 837644754, 77043, "SRX2431093", "SRS1866970", "SRA504806", "GEO", "Kellogg Eye Center, Ophthalmology and Visual Sciences, University of Michigan", 1, 0.88824, null, 0.26531, null, 0.77619, null, 0.64707, null, 52, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-16", "Undetermined", "Adult", "Head", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 304, "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_layout\" = :p0 and \"tissue_curation\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "Head", "p2": "Nervous System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 294, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 287, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&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?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 241, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_selection=cDNA", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_selection=PolyA", "selected": false}, {"value": "other", "label": "other", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_selection=other", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Head&tissue_curation_coarse=Nervous+System&experiment.library_selection=Oligo-dT", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": 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