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
125,DRR189379,DRX179844,DRS200410,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3 / larval zebrafish 5dpf 3,SAMD00182222,,sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182222,DRX179844,Emx3 / Larva body 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,360Application ReadForward1,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182222,,,,1759409208.0,48872478.0,DRR189379,0:36,A:401147348;C:424523813;G:426350919;T:507310828;N:76300,36,,,,401147348,424523813,426350919,507310828,76300,DRX179844,DRS200410,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90975,,0.11439,,0.66076,,0.47775,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
126,DRR189378,DRX179843,DRS200409,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3 / larval zebrafish 5dpf 2,SAMD00182221,,sample name:Emx3 Larva body 2|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182221,DRX179843,Emx3 / Larva body 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,360Application ReadForward1,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182221,,,,1318201020.0,36616695.0,DRR189378,0:36,A:297850068;C:316786585;G:323717530;T:379789606;N:57231,36,,,,297850068,316786585,323717530,379789606,57231,DRX179843,DRS200409,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.9116,,0.11269,,0.65837,,0.46733,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
127,DRR189377,DRX179842,DRS200408,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of EMX3 / larval zebrafish 5dpf 1,SAMD00182220,,sample name:Emx3 Larva body 1|genotype:Emx3 / |tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182220,DRX179842,Emx3 / Larva body 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,360Application ReadForward1,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182220,,,,812483964.0,22568999.0,DRR189377,0:36,A:185173338;C:197790160;G:197482964;T:232000884;N:36618,36,,,,185173338,197790160,197482964,232000884,36618,DRX179842,DRS200408,DRA008857,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.91107,,0.1171,,0.65981,,0.47458,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
128,DRR189376,DRX179841,DRS200449,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 3,SAMD00182219,,sample name:WT Larva body 3|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182219,DRX179841,WT Larva body 3,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,360Application ReadForward1,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182219,,,,4030038144.0,111945504.0,DRR189376,0:36,A:943709984;C:971756680;G:977594500;T:1136798448;N:178532,36,,,,943709984,971756680,977594500,1136798448,178532,DRX179841,DRS200449,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.89574,,0.12331,,0.65831,,0.48096,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
129,DRR189375,DRX179840,DRS200448,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 2,SAMD00182218,,sample name:WT Larva body 2|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182218,DRX179840,WT Larva body 2,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,360Application ReadForward1,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182218,,,,1991670804.0,55324189.0,DRR189375,0:36,A:454367176;C:479012055;G:488407231;T:569793674;N:90668,36,,,,454367176,479012055,488407231,569793674,90668,DRX179840,DRS200448,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.90911,,0.12455,,0.65494,,0.47971,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
130,DRR189374,DRX179839,DRS200447,DRP003977,PRJDB4470,Gene expression analysis of the zebrafish brain,DRP003977,Other,Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.,,,,Whole body of wild type larval zebrafish 5dpf 1,SAMD00182217,,sample name:WT Larva body 1|genotype:wild type|tissue:whole body,,,,,,,,,Illumina HiSeq 3000 sequencing of SAMD00182217,DRX179839,WT Larva body 1,1,SureSelect Strand Specific RNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 3000,360Application ReadForward1,DRP003977,Illumina HiSeq 3000 sequencing of SAMD00182217,,,,1018340100.0,28287225.0,DRR189374,0:36,A:233370050;C:244140659;G:247795084;T:292989542;N:44765,36,,,,233370050,244140659,247795084,292989542,44765,DRX179839,DRS200447,DRA008856,NIG|National Institute of Genetics (Japan),National Institute of Genetics (Japan),1,0.91078,,0.12578,,0.6524,,0.48016,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2021-08-08,Larval,Larval,Trunk,Surface Structure
173,DRR075397,DRX069311,DRS075492,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The remaining part of body of control fish 7dpf,Control body,SAMD00065411,,sample name:1 control body 150701 Hiseq3A l3 017|tissue type:Body,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065411,DRX069311,Control body,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,360Application ReadForward1,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065411,,,,2653100352.0,73697232.0,DRR075397,0:36,A:656791658;C:620507513;G:625038612;T:750671135;N:91434,36,,,,656791658,620507513,625038612,750671135,91434,DRX069311,DRS075492,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.89666,,0.15749,,0.67048,,0.47755,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Trunk,Surface Structure
294,DRR224548,DRX214833,DRS236356,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 28dpf C,SAMD00222579,,sample name:28dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222579,DRX214833,28dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222579,,,,16269568600.0,81347843.0,DRR224548,0:100 1:100,A:3978004953;C:4160626131;G:4174223034;T:3956539398;N:175084,100,100,,,3978004953,4160626131,4174223034,3956539398,175084,DRX214833,DRS236356,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9633,0.95842,0.0474,0.04564,0.72184,0.72253,0.47871,0.46471,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
295,DRR224547,DRX214832,DRS236355,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 28dpf B,SAMD00222578,,sample name:28dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222578,DRX214832,28dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222578,,,,19970979800.0,99854899.0,DRR224547,0:100 1:100,A:5064043525;C:4909415172;G:5303813974;T:4693498507;N:208622,100,100,,,5064043525,4909415172,5303813974,4693498507,208622,DRX214832,DRS236355,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95486,0.94587,0.05718,0.05404,0.73746,0.74754,0.51956,0.47088,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
296,DRR224546,DRX214831,DRS236354,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 28dpf A,SAMD00222577,,sample name:28dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222577,DRX214831,28dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222577,,,,17870876400.0,89354382.0,DRR224546,0:100 1:100,A:4431724830;C:4512913394;G:4543413766;T:4382632384;N:192026,100,100,,,4431724830,4512913394,4543413766,4382632384,192026,DRX214831,DRS236354,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9608,0.95643,0.045,0.04296,0.7236,0.7234,0.50029,0.50287,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
297,DRR224545,DRX214830,DRS236353,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 14dpf C,SAMD00222576,,sample name:14dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222576,DRX214830,14dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222576,,,,16979810200.0,84899051.0,DRR224545,0:100 1:100,A:4241907225;C:4256915446;G:4277991608;T:4202813567;N:182354,100,100,,,4241907225,4256915446,4277991608,4202813567,182354,DRX214830,DRS236353,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96662,0.96168,0.03768,0.03562,0.72368,0.72464,0.48494,0.48687,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
298,DRR224544,DRX214829,DRS236352,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 14dpf B,SAMD00222575,,sample name:14dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222575,DRX214829,14dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222575,,,,18273780000.0,91368900.0,DRR224544,0:100 1:100,A:4545336763;C:4589502978;G:4635310325;T:4503435996;N:193938,100,100,,,4545336763,4589502978,4635310325,4503435996,193938,DRX214829,DRS236352,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97073,0.96595,0.03063,0.02973,0.73632,0.73758,0.47494,0.46918,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
299,DRR224543,DRX214828,DRS236351,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 14dpf A,SAMD00222574,,sample name:14dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222574,DRX214828,14dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222574,,,,18294607600.0,91473038.0,DRR224543,0:100 1:100,A:4623135433;C:4539347940;G:4561846652;T:4570079366;N:198209,100,100,,,4623135433,4539347940,4561846652,4570079366,198209,DRX214828,DRS236351,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96261,0.9592,0.02999,0.02873,0.72699,0.72796,0.4679,0.46591,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
300,DRR224542,DRX214827,DRS236350,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 5dpf C,SAMD00222573,,sample name:5dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222573,DRX214827,5dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222573,,,,18736996000.0,93684980.0,DRR224542,0:100 1:100,A:4647244376;C:4733187951;G:4746515898;T:4609906214;N:141561,100,100,,,4647244376,4733187951,4746515898,4609906214,141561,DRX214827,DRS236350,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97229,0.96893,0.042,0.03995,0.74172,0.74328,0.44607,0.44755,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
301,DRR224541,DRX214826,DRS236349,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 5dpf B,SAMD00222572,,sample name:5dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222572,DRX214826,5dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222572,,,,22151021400.0,110755107.0,DRR224541,0:100 1:100,A:5555093734;C:5532777660;G:5592525988;T:5470461779;N:162239,100,100,,,5555093734,5532777660,5592525988,5470461779,162239,DRX214826,DRS236349,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96835,0.96645,0.04001,0.03872,0.72865,0.72934,0.46355,0.46428,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
302,DRR224540,DRX214825,DRS236348,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 5dpf A,SAMD00222571,,sample name:5dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222571,DRX214825,5dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,2000Application ReadForward11Application ReadReverse101,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222571,,,,18219864200.0,91099321.0,DRR224540,0:100 1:100,A:4485880313;C:4629712312;G:4617351502;T:4486786107;N:133966,100,100,,,4485880313,4629712312,4617351502,4486786107,133966,DRX214825,DRS236348,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97075,0.96902,0.04498,0.0432,0.72971,0.73044,0.45267,0.4604,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
11153,ERR10034052,ERX9574456,ERS12562167,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 5,SAMEA110464139,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464139|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE5|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE5|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:829 19138,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr5.1.fastq.gz S879Nr5.2.fastq.gz,fastq fastq,7308445864.0,36509997.0,ena RUN TAB 05 08 2022 14:25:08:829 19139,0:100.09 1:100.09,A:1934019972;C:1742739870;G:1803466955;T:1828120200;N:98867,100,100,,,1934019972,1742739870,1803466955,1828120200,98867,ERX9574456,ERS12562167,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96596,0.96653,0.05312,0.05284,0.71323,0.71873,0.49632,0.48138,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11154,ERR10034051,ERX9574455,ERS12562166,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 4,SAMEA110464138,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464138|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE4|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE4|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:822 19136,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr4.1.fastq.gz S879Nr4.2.fastq.gz,fastq fastq,8046902370.0,40206331.0,ena RUN TAB 05 08 2022 14:25:08:829 19137,0:100.07 1:100.07,A:2154247315;C:1901540683;G:1965167700;T:2025838764;N:107908,100,100,,,2154247315,1901540683,1965167700,2025838764,107908,ERX9574455,ERS12562166,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.96507,0.96543,0.05345,0.0533,0.71553,0.72123,0.48553,0.49,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11155,ERR10034050,ERX9574454,ERS12562165,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 3,SAMEA110464137,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464137|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE3|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE3|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:821 19134,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr3.1.fastq.gz S879Nr3.2.fastq.gz,fastq fastq,10897526786.0,54442757.0,ena RUN TAB 05 08 2022 14:25:08:821 19135,0:100.08 1:100.08,A:2902340346;C:2590905706;G:2655361716;T:2748771201;N:147817,100,100,,,2902340346,2590905706,2655361716,2748771201,147817,ERX9574454,ERS12562165,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.93244,0.93322,0.04311,0.04269,0.72452,0.72723,0.49726,0.4784,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11156,ERR10034049,ERX9574453,ERS12562164,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 2,SAMEA110464136,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464136|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE2|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE2|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:821 19132,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr2.1.fastq.gz S879Nr2.2.fastq.gz,fastq fastq,8516273680.0,42589650.0,ena RUN TAB 05 08 2022 14:25:08:821 19133,0:99.98 1:99.98,A:2232300748;C:2055212367;G:2121115843;T:2107529926;N:114796,99,99,,,2232300748,2055212367,2121115843,2107529926,114796,ERX9574453,ERS12562164,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.97117,0.97187,0.05876,0.05804,0.72115,0.72689,0.51447,0.50827,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
11157,ERR10034048,ERX9574452,ERS12562163,ERP140005,PRJEB55122,Danio developmental transcriptomes,ca4a518e-aaf7-42d9-9758-352aac808809,Other,Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species.,ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08,,Larval tissue without xxx from Danio rerio,Drerio larval 1,SAMEA110464135,max planck institute for biology,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464135|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE1|collected by:Marco Podobnik|collection date:2018 06 19|common name:zebrafish|dev stage:Larval|identified by:Marco Podobnik|sample name:SAMPLE1|sex:not provided|tissue type:whole body without xxx,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing,ena EXPERIMENT TAB 05 08 2022 14:25:08:820 19130,unspecified,1,Illumina TruSeq DNA Nano Kit,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP140005,Illumina NovaSeq 6000 paired end sequencing,ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08,S879Nr1.1.fastq.gz S879Nr1.2.fastq.gz,fastq fastq,5477863098.0,27332001.0,ena RUN TAB 05 08 2022 14:25:08:821 19131,0:100.21 1:100.21,A:1436230762;C:1320194529;G:1370010454;T:1351352868;N:74485,100,100,,,1436230762,1320194529,1370010454,1351352868,74485,ERX9574452,ERS12562163,ERA16814395,max planck institute for biology|European Nucleotide Archive,max planck institute for biology,2,0.97196,0.97163,0.05932,0.05814,0.72723,0.73348,0.50582,0.51053,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-08-05,Larval,Larval,Trunk,Surface Structure
24600,SRR25475196,SRX21207464,SRS18464933,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],GSM7671235,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671235,GSM7671235: Zebrafish PrP BMD5/50 [PrP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671235 r1,GSM7671235,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_3_1.fq.gz PrP_BMD5_50_3_2.fq.gz,fastq fastq,5877585306.0,19462203.0,GSM7671235 r1,0:151 1:151,A:1673096549;C:1287336870;G:1399452621;T:1517513965;N:185301,151,151,,,1673096549,1287336870,1399452621,1517513965,185301,SRX21207464,SRS18464933,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94721,0.94392,0.10307,0.10285,0.71474,0.7209,0.44676,0.44767,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24601,SRR25475197,SRX21207464,SRS18464933,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],GSM7671235,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671235,GSM7671235: Zebrafish PrP BMD5/50 [PrP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671235 r1,GSM7671235,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_3_3.fq.gz PrP_BMD5_50_3_4.fq.gz,fastq fastq,2592008620.0,8582810.0,GSM7671235 r2,0:151 1:151,A:736893507;C:572181175;G:612346091;T:670582360;N:5487,151,151,,,736893507,572181175,612346091,670582360,5487,SRX21207464,SRS18464933,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94766,0.94372,0.10432,0.10439,0.71108,0.7193,0.4466,0.45067,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24602,SRR25475198,SRX21207463,SRS18464932,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 2],GSM7671234,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671234,GSM7671234: Zebrafish PrP BMD5/50 [PrP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671234 r1,GSM7671234,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_2_1.fq.gz PrP_BMD5_50_2_2.fq.gz,fastq fastq,6523053228.0,21599514.0,GSM7671234 r1,0:151 1:151,A:1881747155;C:1402382759;G:1625853412;T:1612862952;N:206950,151,151,,,1881747155,1402382759,1625853412,1612862952,206950,SRX21207463,SRS18464932,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94694,0.93482,0.08725,0.08666,0.70729,0.72423,0.44992,0.43992,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24603,SRR25475199,SRX21207462,SRS18464931,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],GSM7671233,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671233,GSM7671233: Zebrafish PrP BMD5/50 [PrP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671233 r1,GSM7671233,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_1_1.fq.gz PrP_BMD5_50_1_2.fq.gz,fastq fastq,2090436450.0,6921975.0,GSM7671233 r1,0:151 1:151,A:595082772;C:455110337;G:489835116;T:550342388;N:65837,151,151,,,595082772,455110337,489835116,550342388,65837,SRX21207462,SRS18464931,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.93897,0.93808,0.1192,0.11852,0.71703,0.71938,0.46566,0.48323,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24604,SRR25475200,SRX21207462,SRS18464931,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],GSM7671233,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/50 [PrP BMD5 50 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/50,GSM7671233,GSM7671233: Zebrafish PrP BMD5/50 [PrP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671233 r1,GSM7671233,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_50_1_3.fq.gz PrP_BMD5_50_1_4.fq.gz,fastq fastq,4126091912.0,13662556.0,GSM7671233 r2,0:151 1:151,A:1171476389;C:902866887;G:958669795;T:1093069759;N:9082,151,151,,,1171476389,902866887,958669795,1093069759,9082,SRX21207462,SRS18464931,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.93709,0.93594,0.1203,0.11941,0.71666,0.71924,0.47229,0.47483,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24605,SRR25475201,SRX21207461,SRS18464930,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 3],GSM7671232,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671232,GSM7671232: Zebrafish PrP BMD5/10 [PrP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671232 r1,GSM7671232,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_3_1.fq.gz PrP_BMD5_10_3_2.fq.gz,fastq fastq,6850831646.0,22684873.0,GSM7671232 r1,0:151 1:151,A:1937014178;C:1514493141;G:1623449869;T:1775656465;N:217993,151,151,,,1937014178,1514493141,1623449869,1775656465,217993,SRX21207461,SRS18464930,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94857,0.94727,0.09818,0.0981,0.70849,0.71364,0.44643,0.44849,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24606,SRR25475202,SRX21207460,SRS18464929,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 2],GSM7671231,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671231,GSM7671231: Zebrafish PrP BMD5/10 [PrP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671231 r1,GSM7671231,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_2_2.fq.gz PrP_BMD5_10_2_1.fq.gz,fastq fastq,6143720390.0,20343445.0,GSM7671231 r1,0:151 1:151,A:1724246127;C:1362285676;G:1457061100;T:1599935999;N:191488,151,151,,,1724246127,1362285676,1457061100,1599935999,191488,SRX21207460,SRS18464929,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9488,0.94766,0.094,0.09263,0.70905,0.71348,0.45157,0.43474,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24607,SRR25475203,SRX21207459,SRS18464928,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],GSM7671230,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671230,GSM7671230: Zebrafish PrP BMD5/10 [PrP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671230 r1,GSM7671230,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_1_1.fq.gz PrP_BMD5_10_1_2.fq.gz,fastq fastq,4178827454.0,13837177.0,GSM7671230 r1,0:151 1:151,A:1203579431;C:904927450;G:969023531;T:1101165327;N:131715,151,151,,,1203579431,904927450,969023531,1101165327,131715,SRX21207459,SRS18464928,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94274,0.83776,0.12469,0.10926,0.71752,0.73235,0.47225,0.46096,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24608,SRR25475204,SRX21207459,SRS18464928,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],GSM7671230,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5/10 [PrP BMD5 10 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5/10,GSM7671230,GSM7671230: Zebrafish PrP BMD5/10 [PrP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671230 r1,GSM7671230,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_10_1_4.fq.gz PrP_BMD5_10_1_3.fq.gz,fastq fastq,2952201906.0,9775503.0,GSM7671230 r2,0:151 1:151,A:846361785;C:642990303;G:682081110;T:780762283;N:6425,151,151,,,846361785,642990303,682081110,780762283,6425,SRX21207459,SRS18464928,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9411,0.86904,0.12259,0.11244,0.71392,0.72498,0.47116,0.47213,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24609,SRR25475205,SRX21207458,SRS18464927,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 3],GSM7671229,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671229,GSM7671229: Zebrafish PrP BMD5 [PrP BMD5 3]; Danio rerio; RNA Seq,GSM7671229 r1,GSM7671229,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_3_1.fq.gz PrP_BMD5_3_2.fq.gz,fastq fastq,2629615774.0,8707337.0,GSM7671229 r1,0:151 1:151,A:672958732;C:650029361;G:685902591;T:620641878;N:83212,151,151,,,672958732,650029361,685902591,620641878,83212,SRX21207458,SRS18464927,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.96303,0.96205,0.15116,0.14889,0.74101,0.74548,0.57303,0.57751,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24610,SRR25475206,SRX21207458,SRS18464927,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 3],GSM7671229,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671229,GSM7671229: Zebrafish PrP BMD5 [PrP BMD5 3]; Danio rerio; RNA Seq,GSM7671229 r1,GSM7671229,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_3_3.fq.gz PrP_BMD5_3_4.fq.gz,fastq fastq,3949175782.0,13076741.0,GSM7671229 r2,0:151 1:151,A:1009211118;C:979393371;G:1019201024;T:941361479;N:8790,151,151,,,1009211118,979393371,1019201024,941361479,8790,SRX21207458,SRS18464927,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.96187,0.96117,0.14636,0.14393,0.73813,0.74357,0.55833,0.54801,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24611,SRR25475207,SRX21207457,SRS18464926,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 2],GSM7671228,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671228,GSM7671228: Zebrafish PrP BMD5 [PrP BMD5 2]; Danio rerio; RNA Seq,GSM7671228 r1,GSM7671228,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_2_1.fq.gz PrP_BMD5_2_3.fq.gz,fastq fastq,3744054362.0,12397531.0,GSM7671228 r1,0:151 1:151,A:1046548811;C:825316142;G:923103248;T:948967256;N:118905,151,151,,,1046548811,825316142,923103248,948967256,118905,SRX21207457,SRS18464926,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9498,0.9466,0.09201,0.09131,0.70749,0.71506,0.44879,0.45356,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24612,SRR25475208,SRX21207457,SRS18464926,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 2],GSM7671228,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671228,GSM7671228: Zebrafish PrP BMD5 [PrP BMD5 2]; Danio rerio; RNA Seq,GSM7671228 r1,GSM7671228,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_2_4.fq.gz PrP_BMD5_2_2.fq.gz,fastq fastq,2834446066.0,9385583.0,GSM7671228 r2,0:151 1:151,A:793660024;C:632067365;G:686377801;T:722334752;N:6124,151,151,,,793660024,632067365,686377801,722334752,6124,SRX21207457,SRS18464926,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95049,0.94632,0.09253,0.09174,0.70818,0.71612,0.44666,0.45596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24613,SRR25475209,SRX21207456,SRS18464925,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 1],GSM7671227,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671227,GSM7671227: Zebrafish PrP BMD5 [PrP BMD5 1]; Danio rerio; RNA Seq,GSM7671227 r1,GSM7671227,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_1_1.fq.gz PrP_BMD5_1_2.fq.gz,fastq fastq,3340124530.0,11060015.0,GSM7671227 r1,0:151 1:151,A:957829723;C:716152911;G:809681516;T:856354060;N:106320,151,151,,,957829723,716152911,809681516,856354060,106320,SRX21207456,SRS18464925,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94378,0.93571,0.10991,0.11032,0.71206,0.72214,0.45578,0.44853,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24614,SRR25475210,SRX21207456,SRS18464925,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish PrP BMD5 [PrP BMD5 1],GSM7671227,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5|geo loc name:missing|collection date:missing,Zebrafish PrP BMD5 [PrP BMD5 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:PrP BMD5,GSM7671227,GSM7671227: Zebrafish PrP BMD5 [PrP BMD5 1]; Danio rerio; RNA Seq,GSM7671227 r1,GSM7671227,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,PrP_BMD5_1_3.fq.gz PrP_BMD5_1_4.fq.gz,fastq fastq,2589508060.0,8574530.0,GSM7671227 r2,0:151 1:151,A:743364548;C:559167183;G:621696228;T:665273843;N:6258,151,151,,,743364548,559167183,621696228,665273843,6258,SRX21207456,SRS18464925,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94424,0.93574,0.10895,0.1074,0.70796,0.7189,0.45538,0.45171,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24615,SRR25475211,SRX21207455,SRS18464924,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 3],GSM7671226,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671226,GSM7671226: Zebrafish EtP BMD5/50 [EtP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671226 r1,GSM7671226,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_3_1.fq.gz EtP_BMD5_50_3_2.fq.gz,fastq fastq,12326499346.0,40816223.0,GSM7671226 r1,0:151 1:151,A:3465072251;C:2766110070;G:2948834852;T:3146092010;N:390163,151,151,,,3465072251,2766110070,2948834852,3146092010,390163,SRX21207455,SRS18464924,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95355,0.95009,0.08714,0.08568,0.70782,0.71589,0.45241,0.44173,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24616,SRR25475212,SRX21207454,SRS18464923,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],GSM7671225,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671225,GSM7671225: Zebrafish EtP BMD5/50 [EtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671225 r1,GSM7671225,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_2_1.fq.gz EtP_BMD5_50_2_2.fq.gz,fastq fastq,5873726350.0,19449425.0,GSM7671225 r1,0:151 1:151,A:1639375920;C:1316625633;G:1408239211;T:1509300317;N:185269,151,151,,,1639375920,1316625633,1408239211,1509300317,185269,SRX21207454,SRS18464923,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95095,0.948,0.0908,0.09017,0.70721,0.71224,0.45389,0.44586,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24617,SRR25475213,SRX21207454,SRS18464923,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],GSM7671225,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671225,GSM7671225: Zebrafish EtP BMD5/50 [EtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671225 r1,GSM7671225,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_2_3.fq.gz EtP_BMD5_50_2_4.fq.gz,fastq fastq,2920857930.0,9671715.0,GSM7671225 r2,0:151 1:151,A:813299743;C:659443837;G:696023886;T:752084294;N:6170,151,151,,,813299743,659443837,696023886,752084294,6170,SRX21207454,SRS18464923,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95323,0.94979,0.08949,0.08869,0.70698,0.71352,0.45222,0.45353,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24618,SRR25475214,SRX21207453,SRS18464922,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],GSM7671224,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671224,GSM7671224: Zebrafish EtP BMD5/50 [EtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671224 r1,GSM7671224,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_1_1.fq.gz EtP_BMD5_50_1_2.fq.gz,fastq fastq,3025090814.0,10016857.0,GSM7671224 r1,0:151 1:151,A:843465525;C:670123195;G:725506632;T:785899023;N:96439,151,151,,,843465525,670123195,725506632,785899023,96439,SRX21207453,SRS18464922,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.83589,0.94217,0.09452,0.1077,0.72299,0.71587,0.46107,0.45633,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24619,SRR25475215,SRX21207453,SRS18464922,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],GSM7671224,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/50 [EtP BMD5 50 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/50,GSM7671224,GSM7671224: Zebrafish EtP BMD5/50 [EtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671224 r1,GSM7671224,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_50_1_3.fq.gz EtP_BMD5_50_1_4.fq.gz,fastq fastq,2444467124.0,8094262.0,GSM7671224 r2,0:151 1:151,A:679461384;C:546010997;G:581087164;T:637902414;N:5165,151,151,,,679461384,546010997,581087164,637902414,5165,SRX21207453,SRS18464922,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.87197,0.94213,0.1003,0.10863,0.71616,0.71317,0.45283,0.45457,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24620,SRR25475216,SRX21207452,SRS18464921,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 3],GSM7671223,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671223,GSM7671223: Zebrafish EtP BMD5/10 [EtP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671223 r1,GSM7671223,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_3_1.fq.gz EtP_BMD5_10_3_2.fq.gz,fastq fastq,9653108974.0,31963937.0,GSM7671223 r1,0:151 1:151,A:2697568973;C:2165083953;G:2288959836;T:2501191246;N:304966,151,151,,,2697568973,2165083953,2288959836,2501191246,304966,SRX21207452,SRS18464921,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95172,0.95023,0.08652,0.0862,0.70619,0.71076,0.45447,0.45094,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24621,SRR25475217,SRX21207451,SRS18464920,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],GSM7671222,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671222,GSM7671222: Zebrafish EtP BMD5/10 [EtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671222 r1,GSM7671222,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_2_1.fq.gz EtP_BMD5_10_2_3.fq.gz,fastq fastq,5341647952.0,17687576.0,GSM7671222 r1,0:151 1:151,A:1430194079;C:1246082391;G:1309862164;T:1355339151;N:170167,151,151,,,1430194079,1246082391,1309862164,1355339151,170167,SRX21207451,SRS18464920,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95672,0.95646,0.09343,0.09169,0.715,0.71644,0.44995,0.46948,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24622,SRR25475218,SRX21207451,SRS18464920,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],GSM7671222,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671222,GSM7671222: Zebrafish EtP BMD5/10 [EtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671222 r1,GSM7671222,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_2_2.fq.gz EtP_BMD5_10_2_4.fq.gz,fastq fastq,3095850924.0,10251162.0,GSM7671222 r2,0:151 1:151,A:825080641;C:727003748;G:754816513;T:788943347;N:6675,151,151,,,825080641,727003748,754816513,788943347,6675,SRX21207451,SRS18464920,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95773,0.95746,0.09154,0.09045,0.71145,0.71256,0.46379,0.46536,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24623,SRR25475219,SRX21207450,SRS18464919,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],GSM7671221,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671221,GSM7671221: Zebrafish EtP BMD5/10 [EtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671221 r1,GSM7671221,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_1_1.fq.gz EtP_BMD5_10_1_2.fq.gz,fastq fastq,3224223272.0,10676236.0,GSM7671221 r1,0:151 1:151,A:898136457;C:705998538;G:782593577;T:837393065;N:101635,151,151,,,898136457,705998538,782593577,837393065,101635,SRX21207450,SRS18464919,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94431,0.94367,0.11343,0.11295,0.71238,0.71439,0.46018,0.45575,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24624,SRR25475220,SRX21207450,SRS18464919,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],GSM7671221,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5/10 [EtP BMD5 10 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5/10,GSM7671221,GSM7671221: Zebrafish EtP BMD5/10 [EtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671221 r1,GSM7671221,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_10_1_3.fq.gz EtP_BMD5_10_1_4.fq.gz,fastq fastq,2881317070.0,9540785.0,GSM7671221 r2,0:151 1:151,A:802691268;C:638869913;G:685114354;T:754635149;N:6386,151,151,,,802691268,638869913,685114354,754635149,6386,SRX21207450,SRS18464919,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94507,0.94452,0.11308,0.11253,0.70694,0.71054,0.45347,0.45385,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24625,SRR25475221,SRX21207449,SRS18464918,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 3],GSM7671220,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671220,GSM7671220: Zebrafish EtP BMD5 [EtP BMD5 3]; Danio rerio; RNA Seq,GSM7671220 r1,GSM7671220,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_3_1.fq.gz EtP_BMD5_3_2.fq.gz,fastq fastq,6513209840.0,21566920.0,GSM7671220 r1,0:151 1:151,A:1838683121;C:1445463908;G:1536948771;T:1691910424;N:203616,151,151,,,1838683121,1445463908,1536948771,1691910424,203616,SRX21207449,SRS18464918,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94921,0.94751,0.09226,0.09115,0.70429,0.70907,0.45338,0.45104,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24626,SRR25475222,SRX21207448,SRS18464917,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 2],GSM7671219,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671219,GSM7671219: Zebrafish EtP BMD5 [EtP BMD5 2]; Danio rerio; RNA Seq,GSM7671219 r1,GSM7671219,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_2_1.fq.gz EtP_BMD5_2_2.fq.gz,fastq fastq,4443955368.0,14715084.0,GSM7671219 r1,0:151 1:151,A:1226532150;C:1002488064;G:1058104219;T:1156690900;N:140035,151,151,,,1226532150,1002488064,1058104219,1156690900,140035,SRX21207448,SRS18464917,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95173,0.95111,0.09256,0.09128,0.70469,0.7093,0.44316,0.44626,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24627,SRR25475223,SRX21207448,SRS18464917,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 2],GSM7671219,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671219,GSM7671219: Zebrafish EtP BMD5 [EtP BMD5 2]; Danio rerio; RNA Seq,GSM7671219 r1,GSM7671219,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_2_3.fq.gz EtP_BMD5_2_4.fq.gz,fastq fastq,3368297808.0,11153304.0,GSM7671219 r2,0:151 1:151,A:924217123;C:766145954;G:797666843;T:880260403;N:7485,151,151,,,924217123,766145954,797666843,880260403,7485,SRX21207448,SRS18464917,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95185,0.95089,0.09135,0.08974,0.70453,0.70692,0.44872,0.45596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24628,SRR25475224,SRX21207447,SRS18464916,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 1],GSM7671218,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671218,GSM7671218: Zebrafish EtP BMD5 [EtP BMD5 1]; Danio rerio; RNA Seq,GSM7671218 r1,GSM7671218,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_1_1.fq.gz EtP_BMD5_1_2.fq.gz,fastq fastq,2340650396.0,7750498.0,GSM7671218 r1,0:151 1:151,A:667132609;C:510116860;G:548591619;T:614735275;N:74033,151,151,,,667132609,510116860,548591619,614735275,74033,SRX21207447,SRS18464916,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94031,0.93918,0.11457,0.11486,0.71096,0.71482,0.46017,0.45386,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24629,SRR25475225,SRX21207447,SRS18464916,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish EtP BMD5 [EtP BMD5 1],GSM7671218,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5|geo loc name:missing|collection date:missing,Zebrafish EtP BMD5 [EtP BMD5 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:EtP BMD5,GSM7671218,GSM7671218: Zebrafish EtP BMD5 [EtP BMD5 1]; Danio rerio; RNA Seq,GSM7671218 r1,GSM7671218,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,EtP_BMD5_1_3.fq.gz EtP_BMD5_1_4.fq.gz,fastq fastq,3046691364.0,10088382.0,GSM7671218 r2,0:151 1:151,A:865839573;C:668919023;G:709644830;T:802281652;N:6286,151,151,,,865839573,668919023,709644830,802281652,6286,SRX21207447,SRS18464916,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9416,0.93999,0.11428,0.11391,0.70816,0.71376,0.45095,0.45554,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24630,SRR25475226,SRX21207446,SRS18464915,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],GSM7671217,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671217,GSM7671217: Zebrafish MtP BMD5/50 [MtP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671217 r1,GSM7671217,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_3_2.fq.gz MtP_BMD5_50_3_1.fq.gz,fastq fastq,3653327522.0,12097111.0,GSM7671217 r1,0:151 1:151,A:995366744;C:831318635;G:873618716;T:952906846;N:116581,151,151,,,995366744,831318635,873618716,952906846,116581,SRX21207446,SRS18464915,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95243,0.95252,0.09088,0.08971,0.7167,0.71711,0.45455,0.44644,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24631,SRR25475227,SRX21207446,SRS18464915,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],GSM7671217,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671217,GSM7671217: Zebrafish MtP BMD5/50 [MtP BMD5 50 3]; Danio rerio; RNA Seq,GSM7671217 r1,GSM7671217,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_3_3.fq.gz MtP_BMD5_50_3_4.fq.gz,fastq fastq,3423528474.0,11336187.0,GSM7671217 r2,0:151 1:151,A:928366145;C:784910903;G:813824790;T:896419194;N:7442,151,151,,,928366145,784910903,813824790,896419194,7442,SRX21207446,SRS18464915,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95366,0.9537,0.08926,0.08783,0.71423,0.71488,0.44252,0.44528,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24632,SRR25475228,SRX21207445,SRS18464914,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],GSM7671216,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671216,GSM7671216: Zebrafish MtP BMD5/50 [MtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671216 r1,GSM7671216,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_2_1.fq.gz MtP_BMD5_50_2_2.fq.gz,fastq fastq,4942474922.0,16365811.0,GSM7671216 r1,0:151 1:151,A:1353408937;C:1120658999;G:1177996657;T:1290253217;N:157112,151,151,,,1353408937,1120658999,1177996657,1290253217,157112,SRX21207445,SRS18464914,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95342,0.9531,0.08768,0.0872,0.71603,0.71741,0.4477,0.45194,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24633,SRR25475229,SRX21207445,SRS18464914,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],GSM7671216,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671216,GSM7671216: Zebrafish MtP BMD5/50 [MtP BMD5 50 2]; Danio rerio; RNA Seq,GSM7671216 r1,GSM7671216,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_2_4.fq.gz MtP_BMD5_50_2_3.fq.gz,fastq fastq,3002985622.0,9943661.0,GSM7671216 r2,0:151 1:151,A:819177253;C:685416613;G:712807034;T:785577695;N:7027,151,151,,,819177253,685416613,712807034,785577695,7027,SRX21207445,SRS18464914,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95358,0.95373,0.08626,0.08506,0.71539,0.71737,0.44723,0.45008,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24634,SRR25475230,SRX21207444,SRS18464913,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],GSM7671215,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671215,GSM7671215: Zebrafish MtP BMD5/50 [MtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671215 r1,GSM7671215,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_1_1.fq.gz MtP_BMD5_50_1_2.fq.gz,fastq fastq,5572679764.0,18452582.0,GSM7671215 r1,0:151 1:151,A:1572978393;C:1231505384;G:1304580144;T:1463439694;N:176149,151,151,,,1572978393,1231505384,1304580144,1463439694,176149,SRX21207444,SRS18464913,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94618,0.94569,0.10995,0.10957,0.71208,0.71577,0.44248,0.45317,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24635,SRR25475231,SRX21207444,SRS18464913,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],GSM7671215,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/50 [MtP BMD5 50 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/50,GSM7671215,GSM7671215: Zebrafish MtP BMD5/50 [MtP BMD5 50 1]; Danio rerio; RNA Seq,GSM7671215 r1,GSM7671215,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_50_1_3.fq.gz MtP_BMD5_50_1_4.fq.gz,fastq fastq,3433554572.0,11369386.0,GSM7671215 r2,0:151 1:151,A:966269363;C:763349843;G:801297479;T:902630496;N:7391,151,151,,,966269363,763349843,801297479,902630496,7391,SRX21207444,SRS18464913,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94553,0.94332,0.10986,0.10805,0.70989,0.71388,0.45838,0.45123,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24636,SRR25475232,SRX21207443,SRS18464912,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],GSM7671214,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671214,GSM7671214: Zebrafish MtP BMD5/10 [MtP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671214 r1,GSM7671214,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_3_1.fq.gz MtP_BMD5_10_3_2.fq.gz,fastq fastq,5569270486.0,18441293.0,GSM7671214 r1,0:151 1:151,A:1574836056;C:1234020787;G:1290444481;T:1469794057;N:175105,151,151,,,1574836056,1234020787,1290444481,1469794057,175105,SRX21207443,SRS18464912,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95004,0.94806,0.10109,0.10024,0.71088,0.71415,0.45842,0.43735,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24637,SRR25475233,SRX21207443,SRS18464912,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],GSM7671214,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671214,GSM7671214: Zebrafish MtP BMD5/10 [MtP BMD5 10 3]; Danio rerio; RNA Seq,GSM7671214 r1,GSM7671214,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_3_3.fq.gz MtP_BMD5_10_3_4.fq.gz,fastq fastq,2514406700.0,8325850.0,GSM7671214 r2,0:151 1:151,A:708216865;C:560027758;G:582256307;T:663900270;N:5500,151,151,,,708216865,560027758,582256307,663900270,5500,SRX21207443,SRS18464912,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94944,0.94814,0.10054,0.10067,0.70751,0.71246,0.45622,0.44451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24638,SRR25475234,SRX21207442,SRS18464911,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],GSM7671213,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671213,GSM7671213: Zebrafish MtP BMD5/10 [MtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671213 r1,GSM7671213,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_2_1.fq.gz MtP_BMD5_10_2_2.fq.gz,fastq fastq,3506823396.0,11611998.0,GSM7671213 r1,0:151 1:151,A:982455627;C:781917114;G:848218674;T:894124856;N:107125,151,151,,,982455627,781917114,848218674,894124856,107125,SRX21207442,SRS18464911,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9504,0.94715,0.09519,0.09469,0.71147,0.718,0.44922,0.43458,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24639,SRR25475235,SRX21207442,SRS18464911,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],GSM7671213,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671213,GSM7671213: Zebrafish MtP BMD5/10 [MtP BMD5 10 2]; Danio rerio; RNA Seq,GSM7671213 r1,GSM7671213,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_2_3.fq.gz MtP_BMD5_10_2_4.fq.gz,fastq fastq,2523360094.0,8355497.0,GSM7671213 r2,0:151 1:151,A:705451559;C:567104395;G:605344307;T:645454842;N:4991,151,151,,,705451559,567104395,605344307,645454842,4991,SRX21207442,SRS18464911,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95062,0.94751,0.09472,0.094,0.71005,0.71666,0.45245,0.44889,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24640,SRR25475236,SRX21207441,SRS18464910,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],GSM7671212,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671212,GSM7671212: Zebrafish MtP BMD5/10 [MtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671212 r1,GSM7671212,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_1_1.fq.gz MtP_BMD5_10_1_2.fq.gz,fastq fastq,4528464330.0,14994915.0,GSM7671212 r1,0:151 1:151,A:1261030694;C:1015640347;G:1058184835;T:1193464002;N:144452,151,151,,,1261030694,1015640347,1058184835,1193464002,144452,SRX21207441,SRS18464910,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9473,0.94598,0.11708,0.11509,0.71364,0.71522,0.4646,0.46444,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24641,SRR25475237,SRX21207441,SRS18464910,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],GSM7671212,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5/10 [MtP BMD5 10 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5/10,GSM7671212,GSM7671212: Zebrafish MtP BMD5/10 [MtP BMD5 10 1]; Danio rerio; RNA Seq,GSM7671212 r1,GSM7671212,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_10_1_3.fq.gz MtP_BMD5_10_1_4.fq.gz,fastq fastq,2980367030.0,9868765.0,GSM7671212 r2,0:151 1:151,A:825558450;C:671536928;G:694866440;T:788398550;N:6662,151,151,,,825558450,671536928,694866440,788398550,6662,SRX21207441,SRS18464910,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94762,0.9469,0.11432,0.11281,0.71001,0.71297,0.46658,0.45541,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24642,SRR25475238,SRX21207440,SRS18464909,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 3],GSM7671211,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671211,GSM7671211: Zebrafish MtP BMD5 [MtP BMD5 3]; Danio rerio; RNA Seq,GSM7671211 r1,GSM7671211,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_3_1.fq.gz MtP_BMD5_3_2.fq.gz,fastq fastq,4936487470.0,16345985.0,GSM7671211 r1,0:151 1:151,A:1378752654;C:1113742094;G:1158863879;T:1284972892;N:155951,151,151,,,1378752654,1113742094,1158863879,1284972892,155951,SRX21207440,SRS18464909,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95301,0.95122,0.0955,0.0941,0.71208,0.71648,0.44704,0.44817,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24643,SRR25475239,SRX21207440,SRS18464909,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 3],GSM7671211,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671211,GSM7671211: Zebrafish MtP BMD5 [MtP BMD5 3]; Danio rerio; RNA Seq,GSM7671211 r1,GSM7671211,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_3_3.fq.gz MtP_BMD5_3_4.fq.gz,fastq fastq,3298411686.0,10921893.0,GSM7671211 r2,0:151 1:151,A:917164468;C:748498488;G:774036441;T:858705230;N:7059,151,151,,,917164468,748498488,774036441,858705230,7059,SRX21207440,SRS18464909,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95205,0.95054,0.09425,0.09329,0.71011,0.71455,0.44566,0.44912,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24644,SRR25475240,SRX21207439,SRS18464908,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 2],GSM7671210,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671210,GSM7671210: Zebrafish MtP BMD5 [MtP BMD5 2]; Danio rerio; RNA Seq,GSM7671210 r1,GSM7671210,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_2_1.fq.gz MtP_BMD5_2_2.fq.gz,fastq fastq,6227362008.0,20620404.0,GSM7671210 r1,0:151 1:151,A:1715937364;C:1386359386;G:1515578719;T:1609287962;N:198577,151,151,,,1715937364,1386359386,1515578719,1609287962,198577,SRX21207439,SRS18464908,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.9491,0.94828,0.10169,0.10078,0.71399,0.71605,0.45429,0.454,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24645,SRR25475241,SRX21207438,SRS18464907,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 1],GSM7671209,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671209,GSM7671209: Zebrafish MtP BMD5 [MtP BMD5 1]; Danio rerio; RNA Seq,GSM7671209 r1,GSM7671209,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_1_1.fq.gz MtP_BMD5_1_4.fq.gz,fastq fastq,4052874428.0,13420114.0,GSM7671209 r1,0:151 1:151,A:1131227099;C:867529007;G:1014888508;T:1039101737;N:128077,151,151,,,1131227099,867529007,1014888508,1039101737,128077,SRX21207438,SRS18464907,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94427,0.94289,0.11676,0.11646,0.71587,0.72013,0.4544,0.45822,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24646,SRR25475242,SRX21207438,SRS18464907,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish MtP BMD5 [MtP BMD5 1],GSM7671209,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing,Zebrafish MtP BMD5 [MtP BMD5 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5,GSM7671209,GSM7671209: Zebrafish MtP BMD5 [MtP BMD5 1]; Danio rerio; RNA Seq,GSM7671209 r1,GSM7671209,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,MtP_BMD5_1_2.fq.gz MtP_BMD5_1_3.fq.gz,fastq fastq,3419102060.0,11321530.0,GSM7671209 r2,0:151 1:151,A:962312797;C:746662074;G:817866377;T:892253758;N:7054,151,151,,,962312797,746662074,817866377,892253758,7054,SRX21207438,SRS18464907,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94437,0.94159,0.11604,0.11533,0.7122,0.71697,0.45308,0.45718,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24647,SRR25475243,SRX21207437,SRS18464906,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 3],GSM7671208,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671208,GSM7671208: Zebrafish Control [C 3]; Danio rerio; RNA Seq,GSM7671208 r1,GSM7671208,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_3_1.fq.gz C_3_2.fq.gz,fastq fastq,5057829560.0,16747780.0,GSM7671208 r1,0:151 1:151,A:1402165693;C:1118939077;G:1238989668;T:1297578003;N:157119,151,151,,,1402165693,1118939077,1238989668,1297578003,157119,SRX21207437,SRS18464906,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95294,0.95134,0.09354,0.09252,0.71758,0.72255,0.44734,0.44399,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24648,SRR25475244,SRX21207437,SRS18464906,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 3],GSM7671208,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 3],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671208,GSM7671208: Zebrafish Control [C 3]; Danio rerio; RNA Seq,GSM7671208 r1,GSM7671208,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_3_3.fq.gz C_3_4.fq.gz,fastq fastq,2444105026.0,8093063.0,GSM7671208 r2,0:151 1:151,A:677519922;C:547933936;G:588011673;T:630634167;N:5328,151,151,,,677519922,547933936,588011673,630634167,5328,SRX21207437,SRS18464906,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95279,0.95095,0.09225,0.09186,0.71532,0.72021,0.44267,0.42467,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24649,SRR25475245,SRX21207436,SRS18464905,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 2],GSM7671207,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 2],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671207,GSM7671207: Zebrafish Control [C 2]; Danio rerio; RNA Seq,GSM7671207 r1,GSM7671207,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_2_1.fq.gz C_2_2.fq.gz,fastq fastq,6798305692.0,22510946.0,GSM7671207 r1,0:151 1:151,A:1815427330;C:1575068301;G:1689634001;T:1717960363;N:215697,151,151,,,1815427330,1575068301,1689634001,1717960363,215697,SRX21207436,SRS18464905,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.95273,0.95222,0.10352,0.10219,0.71806,0.71952,0.468,0.47405,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24650,SRR25475246,SRX21207435,SRS18464904,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 1],GSM7671206,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671206,GSM7671206: Zebrafish Control [C 1]; Danio rerio; RNA Seq,GSM7671206 r1,GSM7671206,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_1_1.fq.gz C_1_2.fq.gz,fastq fastq,4775780888.0,15813844.0,GSM7671206 r1,0:151 1:151,A:1349640328;C:1033890598;G:1150153417;T:1241944276;N:152269,151,151,,,1349640328,1033890598,1150153417,1241944276,152269,SRX21207435,SRS18464904,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.93975,0.93846,0.11061,0.11057,0.70796,0.7122,0.45018,0.4485,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24651,SRR25475247,SRX21207435,SRS18464904,SRP452529,PRJNA1000943,Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos,GSE239773,Transcriptome Analysis,"Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through ""the Technology Development Project for Safety Management of Household Chemical Products"" funded by Korea Ministry of Environment MOE grant number 2020002960006.",,,,Zebrafish Control [C 1],GSM7671206,,source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control|geo loc name:missing|collection date:missing,Zebrafish Control [C 1],Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values,Whole body,,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:Control,GSM7671206,GSM7671206: Zebrafish Control [C 1]; Danio rerio; RNA Seq,GSM7671206 r1,GSM7671206,1,The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP452529,,loader:fastq load.py,C_1_3.fq.gz C_1_4.fq.gz,fastq fastq,2235109248.0,7401024.0,GSM7671206 r2,0:151 1:151,A:630617292;C:490828084;G:527489424;T:586169387;N:5061,151,151,,,630617292,490828084,527489424,586169387,5061,SRX21207435,SRS18464904,SRA1684601,Seoul National University of Science and Technology,Seoul National University of Science and Technology,2,0.94126,0.94112,0.10981,0.11011,0.70485,0.70995,0.44139,0.45284,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,South Korea,2023-08-01,Larval,Larval,Trunk,Surface Structure
24906,SRR25532497,SRX21261798,SRS18515093,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.42 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S10,S10,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK1_1.fq.gz CK1_2.fq.gz,fastq fastq,6650697900.0,22168993.0,CK1 1.fq.gz,0:150 1:150,A:1918460669;C:1420936092;G:1412569553;T:1898656995;N:74591,150,150,,,1918460669,1420936092,1412569553,1898656995,74591,SRX21261798,SRS18515093,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.91765,0.91694,0.15569,0.15461,0.70185,0.7027,0.47761,0.47369,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24907,SRR25532498,SRX21261797,SRS18515092,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.41 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S9,S9,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH3_2.fq.gz MBTH3_1.fq.gz,fastq fastq,6333332100.0,21111107.0,MBTH3 1.fq.gz,0:150 1:150,A:1755718187;C:1429192980;G:1420776066;T:1727550080;N:94787,150,150,,,1755718187,1429192980,1420776066,1727550080,94787,SRX21261797,SRS18515092,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93518,0.93355,0.11668,0.11602,0.67799,0.67817,0.47705,0.47875,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24908,SRR25532499,SRX21261796,SRS18515091,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.40 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S8,S8,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH2_1.fq.gz MBTH2_2.fq.gz,fastq fastq,6373733400.0,21245778.0,MBTH2 1.fq.gz,0:150 1:150,A:1775132718;C:1430955007;G:1424605018;T:1742942742;N:97915,150,150,,,1775132718,1430955007,1424605018,1742942742,97915,SRX21261796,SRS18515091,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93081,0.93016,0.12061,0.11947,0.68215,0.68172,0.47956,0.48186,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24909,SRR25532500,SRX21261795,SRS18515090,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTH1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.39 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S7,S7,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTH1_1.fq.gz MBTH1_2.fq.gz,fastq fastq,6224052600.0,20746842.0,MBTH1 1.fq.gz,0:150 1:150,A:1753175301;C:1379045823;G:1371537072;T:1720226102;N:68302,150,150,,,1753175301,1379045823,1371537072,1720226102,68302,SRX21261795,SRS18515090,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.9276,0.92379,0.13642,0.13482,0.68416,0.68479,0.47638,0.47581,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24910,SRR25532501,SRX21261794,SRS18515089,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.38 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S6,S6,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM3_2.fq.gz MBTM3_1.fq.gz,fastq fastq,6885667800.0,22952226.0,MBTM3 1.fq.gz,0:150 1:150,A:1936367424;C:1526831248;G:1520656271;T:1901736749;N:76108,150,150,,,1936367424,1526831248,1520656271,1901736749,76108,SRX21261794,SRS18515089,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92736,0.92516,0.12801,0.12693,0.68982,0.69063,0.47163,0.4612,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24911,SRR25532502,SRX21261793,SRS18515088,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.37 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S5,S5,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM2_1.fq.gz MBTM2_2.fq.gz,fastq fastq,6529427400.0,21764758.0,MBTM2 1.fq.gz,0:150 1:150,A:1808908277;C:1472638598;G:1467975655;T:1779801002;N:103868,150,150,,,1808908277,1472638598,1467975655,1779801002,103868,SRX21261793,SRS18515088,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.9296,0.93217,0.11772,0.11735,0.68262,0.68331,0.4724,0.4721,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24912,SRR25532503,SRX21261792,SRS18515087,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTM1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.36 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S4,S4,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTM1_2.fq.gz MBTM1_1.fq.gz,fastq fastq,6733924800.0,22446416.0,MBTM1 1.fq.gz,0:150 1:150,A:1847490053;C:1535661831;G:1528806965;T:1821868439;N:97512,150,150,,,1847490053,1535661831,1528806965,1821868439,97512,SRX21261792,SRS18515087,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93177,0.93448,0.11165,0.11192,0.67722,0.67823,0.47325,0.46912,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24913,SRR25532504,SRX21261791,SRS18515086,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.35 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S3,S3,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL3_1.fq.gz MBTL3_2.fq.gz,fastq fastq,9066238500.0,30220795.0,MBTL3 1.fq.gz,0:150 1:150,A:2629692873;C:1932648084;G:1927694770;T:2576111685;N:91088,150,150,,,2629692873,1932648084,1927694770,2576111685,91088,SRX21261791,SRS18515086,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.93079,0.91809,0.1476,0.14446,0.69201,0.69258,0.47663,0.47687,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24914,SRR25532505,SRX21261790,SRS18515085,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.44 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S12,S12,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK3_1.fq.gz CK3_2.fq.gz,fastq fastq,6596041200.0,21986804.0,CK3 1.fq.gz,0:150 1:150,A:1886076947;C:1431757712;G:1423068767;T:1855067482;N:70292,150,150,,,1886076947,1431757712,1423068767,1855067482,70292,SRX21261790,SRS18515085,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92168,0.92147,0.14797,0.14768,0.68962,0.68935,0.47874,0.48307,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24915,SRR25532506,SRX21261789,SRS18515084,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,control2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.43 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S11,S11,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,CK2_1.fq.gz CK2_2.fq.gz,fastq fastq,6749651400.0,22498838.0,CK2 1.fq.gz,0:150 1:150,A:1934306700;C:1451979582;G:1445551014;T:1917740723;N:73381,150,150,,,1934306700,1451979582,1445551014,1917740723,73381,SRX21261789,SRS18515084,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92261,0.92062,0.15096,0.14969,0.69783,0.69702,0.48303,0.49016,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24916,SRR25532507,SRX21261788,SRS18515083,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.34 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S2,S2,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL2_1.fq.gz MBTL2_2.fq.gz,fastq fastq,6868354800.0,22894516.0,MBTL2 1.fq.gz,0:150 1:150,A:1956017484;C:1493585329;G:1486220640;T:1932456728;N:74619,150,150,,,1956017484,1493585329,1486220640,1932456728,74619,SRX21261788,SRS18515083,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92126,0.91908,0.14701,0.14525,0.69394,0.69363,0.47281,0.47636,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
24917,SRR25532508,SRX21261787,SRS18515082,SRP453533,PRJNA1002570,MBT induced effects in zebrafish eyes,PRJNA1002570,Other,We intended to screen the key events in zebrafish larvae post MBT exposure.,,,,,MBTL1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.33 E|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of fish,S1,S1,normal RNAseq of fish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP453533,,,MBTL1_1.fq.gz MBTL1_2.fq.gz,fastq fastq,6305127900.0,21017093.0,MBTL1 1.fq.gz,0:150 1:150,A:1797030982;C:1364002775;G:1357954929;T:1786051425;N:87789,150,150,,,1797030982,1364002775,1357954929,1786051425,87789,SRX21261787,SRS18515082,SRA1687160,Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES,Chinese Academy of Sciences,2,0.92195,0.92138,0.14404,0.1433,0.69656,0.69623,0.47185,0.46936,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-08-05,Undetermined,Larval,Trunk,Surface Structure
25329,SRR25868071,SRX21589492,SRS18767065,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP4,GSM7749557,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP4,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749557,GSM7749557: sibCGFP4; Danio rerio; RNA Seq,GSM7749557 r1,GSM7749557,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP4_S46_L002_R1_001.fastq.gz WA-3548-sibCGFP4_S46_L002_R2_001.fastq.gz,fastq fastq,11996252984.0,39722692.0,GSM7749557 r1,0:151 1:151,A:3208564840;C:2791941387;G:2921724669;T:3073456372;N:565716,151,151,,,3208564840,2791941387,2921724669,3073456372,565716,SRX21589492,SRS18767065,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96224,0.96334,0.07442,0.07372,0.70595,0.70688,0.47053,0.46853,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25330,SRR25868072,SRX21589491,SRS18767064,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP3,GSM7749556,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP3,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749556,GSM7749556: sibCGFP3; Danio rerio; RNA Seq,GSM7749556 r1,GSM7749556,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP3_S45_L002_R1_001.fastq.gz WA-3548-sibCGFP3_S45_L002_R2_001.fastq.gz,fastq fastq,10113421300.0,33488150.0,GSM7749556 r1,0:151 1:151,A:2677217319;C:2366433560;G:2481164832;T:2588131881;N:473708,151,151,,,2677217319,2366433560,2481164832,2588131881,473708,SRX21589491,SRS18767064,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96295,0.96335,0.07275,0.07118,0.70654,0.7092,0.45672,0.44027,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25331,SRR25868073,SRX21589490,SRS18767063,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP2,GSM7749555,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP2,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749555,GSM7749555: sibCGFP2; Danio rerio; RNA Seq,GSM7749555 r1,GSM7749555,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP2_S44_L002_R1_001.fastq.gz WA-3548-sibCGFP2_S44_L002_R2_001.fastq.gz,fastq fastq,10142198578.0,33583439.0,GSM7749555 r1,0:151 1:151,A:2687719512;C:2375571494;G:2493046337;T:2585391111;N:470124,151,151,,,2687719512,2375571494,2493046337,2585391111,470124,SRX21589490,SRS18767063,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96241,0.96294,0.07398,0.07262,0.70524,0.70589,0.45777,0.46014,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25332,SRR25868074,SRX21589489,SRS18767062,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP1,GSM7749554,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP1,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749554,GSM7749554: sibCGFP1; Danio rerio; RNA Seq,GSM7749554 r1,GSM7749554,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP1_S43_L002_R1_001.fastq.gz WA-3548-sibCGFP1_S43_L002_R2_001.fastq.gz,fastq fastq,10994030650.0,36404075.0,GSM7749554 r1,0:151 1:151,A:2911908895;C:2573164804;G:2700790583;T:2807654156;N:512212,151,151,,,2911908895,2573164804,2700790583,2807654156,512212,SRX21589489,SRS18767062,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96119,0.96215,0.07361,0.07253,0.70632,0.7069,0.45503,0.45981,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25333,SRR25868075,SRX21589488,SRS18767059,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC4,GSM7749553,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC4,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749553,GSM7749553: sibC4; Danio rerio; RNA Seq,GSM7749553 r1,GSM7749553,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC4_S42_L002_R1_001.fastq.gz WA-3548-sibC4_S42_L002_R2_001.fastq.gz,fastq fastq,11107320816.0,36779208.0,GSM7749553 r1,0:151 1:151,A:2945889871;C:2588267204;G:2719520712;T:2853118433;N:524596,151,151,,,2945889871,2588267204,2719520712,2853118433,524596,SRX21589488,SRS18767059,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96098,0.96213,0.07535,0.07463,0.70623,0.70749,0.42034,0.43255,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25334,SRR25868076,SRX21589487,SRS18767060,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC3,GSM7749552,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC3,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749552,GSM7749552: sibC3; Danio rerio; RNA Seq,GSM7749552 r1,GSM7749552,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC3_S41_L002_R1_001.fastq.gz WA-3548-sibC3_S41_L002_R2_001.fastq.gz,fastq fastq,12566811014.0,41611957.0,GSM7749552 r1,0:151 1:151,A:3330340903;C:2960050871;G:3087690864;T:3188143295;N:585081,151,151,,,3330340903,2960050871,3087690864,3188143295,585081,SRX21589487,SRS18767060,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9619,0.96201,0.08592,0.08414,0.69581,0.69637,0.47091,0.47561,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25335,SRR25868077,SRX21589486,SRS18767057,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC2,GSM7749551,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC2,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749551,GSM7749551: sibC2; Danio rerio; RNA Seq,GSM7749551 r1,GSM7749551,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC2_S40_L002_R1_001.fastq.gz WA-3548-sibC2_S40_L002_R2_001.fastq.gz,fastq fastq,9464242402.0,31338551.0,GSM7749551 r1,0:151 1:151,A:2497543137;C:2235078067;G:2319534414;T:2411649747;N:437037,151,151,,,2497543137,2235078067,2319534414,2411649747,437037,SRX21589486,SRS18767057,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96464,0.965,0.06696,0.06563,0.7138,0.71512,0.46359,0.46601,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25336,SRR25868078,SRX21589485,SRS18767061,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC1,GSM7749550,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC1,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749550,GSM7749550: sibC1; Danio rerio; RNA Seq,GSM7749550 r1,GSM7749550,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-sibC1_S39_L002_R1_001.fastq.gz WA-3548-sibC1_S39_L002_R2_001.fastq.gz,fastq fastq,11153872908.0,36933354.0,GSM7749550 r1,0:151 1:151,A:2966120106;C:2600333644;G:2710289968;T:2876608337;N:520853,151,151,,,2966120106,2600333644,2710289968,2876608337,520853,SRX21589485,SRS18767061,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96189,0.96306,0.07632,0.07512,0.70749,0.70818,0.46784,0.4683,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25337,SRR25868079,SRX21589484,SRS18767058,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP4,GSM7749549,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP4,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749549,GSM7749549: dmdGFP4; Danio rerio; RNA Seq,GSM7749549 r1,GSM7749549,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP4_S54_L002_R1_001.fastq.gz WA-3548-dmdGFP4_S54_L002_R2_001.fastq.gz,fastq fastq,6593937762.0,21834231.0,GSM7749549 r1,0:151 1:151,A:1745786828;C:1531704556;G:1637507801;T:1678632967;N:305610,151,151,,,1745786828,1531704556,1637507801,1678632967,305610,SRX21589484,SRS18767058,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9626,0.96282,0.08653,0.08533,0.70433,0.70636,0.47707,0.46994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25338,SRR25868080,SRX21589483,SRS18767056,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP3,GSM7749548,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP3,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749548,GSM7749548: dmdGFP3; Danio rerio; RNA Seq,GSM7749548 r1,GSM7749548,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP3_S53_L002_R1_001.fastq.gz WA-3548-dmdGFP3_S53_L002_R2_001.fastq.gz,fastq fastq,9250573476.0,30631038.0,GSM7749548 r1,0:151 1:151,A:2485551140;C:2135752367;G:2259698711;T:2369143289;N:427969,151,151,,,2485551140,2135752367,2259698711,2369143289,427969,SRX21589483,SRS18767056,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96118,0.96196,0.0946,0.09271,0.69702,0.69834,0.47168,0.47515,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25339,SRR25868081,SRX21589482,SRS18767055,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP2,GSM7749547,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP2,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749547,GSM7749547: dmdGFP2; Danio rerio; RNA Seq,GSM7749547 r1,GSM7749547,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP2_S52_L002_R1_001.fastq.gz WA-3548-dmdGFP2_S52_L002_R2_001.fastq.gz,fastq fastq,8584886654.0,28426777.0,GSM7749547 r1,0:151 1:151,A:2310205296;C:1982936514;G:2071907465;T:2219441471;N:395908,151,151,,,2310205296,1982936514,2071907465,2219441471,395908,SRX21589482,SRS18767055,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9586,0.95966,0.09636,0.09473,0.69881,0.6997,0.47446,0.47409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25340,SRR25868082,SRX21589481,SRS18767052,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP1,GSM7749546,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP1,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749546,GSM7749546: dmdGFP1; Danio rerio; RNA Seq,GSM7749546 r1,GSM7749546,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP1_S51_L002_R1_001.fastq.gz WA-3548-dmdGFP1_S51_L002_R2_001.fastq.gz,fastq fastq,7573189674.0,25076787.0,GSM7749546 r1,0:151 1:151,A:2025587174;C:1735604560;G:1848622101;T:1963022142;N:353697,151,151,,,2025587174,1735604560,1848622101,1963022142,353697,SRX21589481,SRS18767052,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.95942,0.96073,0.08752,0.08624,0.69863,0.69822,0.4733,0.47454,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25341,SRR25868083,SRX21589480,SRS18767054,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd4,GSM7749545,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd4,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749545,GSM7749545: dmd4; Danio rerio; RNA Seq,GSM7749545 r1,GSM7749545,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd4_S50_L002_R1_001.fastq.gz WA-3548-dmd4_S50_L002_R2_001.fastq.gz,fastq fastq,9121652998.0,30204149.0,GSM7749545 r1,0:151 1:151,A:2438907102;C:2114952319;G:2225797925;T:2341561511;N:434141,151,151,,,2438907102,2114952319,2225797925,2341561511,434141,SRX21589480,SRS18767054,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.961,0.96258,0.08366,0.08276,0.69787,0.69856,0.47181,0.46112,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25342,SRR25868084,SRX21589479,SRS18767053,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd3,GSM7749544,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd3,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749544,GSM7749544: dmd3; Danio rerio; RNA Seq,GSM7749544 r1,GSM7749544,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd3_S49_L002_R1_001.fastq.gz WA-3548-dmd3_S49_L002_R2_001.fastq.gz,fastq fastq,7896671538.0,26147919.0,GSM7749544 r1,0:151 1:151,A:2104101125;C:1828908837;G:1933039401;T:2030257090;N:365085,151,151,,,2104101125,1828908837,1933039401,2030257090,365085,SRX21589479,SRS18767053,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96014,0.96084,0.08575,0.08475,0.70082,0.70108,0.47254,0.47153,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25343,SRR25868085,SRX21589478,SRS18767051,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,Transcriptome Analysis,In muscle dystrophies muscle fibers loose integrity and die leading to significant suffering and a shorter life. Strikingly the extraocular muscles EOMs controlling eye movements are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin plectin and obscurin intermediate filament proteins causing different muscle dystrophies and contributes to disease protection of the EOMs. Moreover we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje significantly improving their survival rate. Therefore fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd2,GSM7749543,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd2,Sequence reads were mapped to GRCz11 using STAR options: outSAMtype BAM SortedByCoordinate seedSearchStartLmax 12 outFilterScoreMinOverLread 0.3 alignSJoverhangMin 15 outFilterMismatchNmax 33 outFilterMatchNminOverLread 0 outFilterType BySJout outSAMunmapped Within outSAMattributes NH HI AS NM MD outSAMstrandField intronMotif quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,5 dpf trunk,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb / double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749543,GSM7749543: dmd2; Danio rerio; RNA Seq,GSM7749543 r1,GSM7749543,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at 80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457981,,loader:fastq load.py,WA-3548-dmd2_S48_L002_R1_001.fastq.gz WA-3548-dmd2_S48_L002_R2_001.fastq.gz,fastq fastq,9484006792.0,31403996.0,GSM7749543 r1,0:151 1:151,A:2518758838;C:2211640185;G:2303907076;T:2449259369;N:441324,151,151,,,2518758838,2211640185,2303907076,2449259369,441324,SRX21589478,SRS18767051,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96047,0.96128,0.09081,0.09031,0.69603,0.69605,0.46706,0.47077,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure