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 66124,SRR15927835,SRX12217977,SRS10194181,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate4,,0.1MPa Muscle 4,,strain:11|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,0.1MPa Muscle 4,0.1MPa Muscle 4,0.1MPa Muscle 4,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,0.1MPa_Muscle_4_1.fq.gz 0.1MPa_Muscle_4_2.fq.gz,fastq fastq,10711204800.0,35704016.0,0.1MPa Muscle 4 1.fq.gz,0:150 1:150,A:2765555622;C:2606137694;G:2609874691;T:2729600138;N:36655,150,150,,,2765555622,2606137694,2609874691,2729600138,36655,SRX12217977,SRS10194181,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.9603,0.95992,0.029,0.02943,0.79912,0.80044,0.51095,0.51424,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66127,SRR15927793,SRX12217974,SRS10194177,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate3,,0.1MPa Muscle 3,,strain:10|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,0.1MPa Muscle 3,0.1MPa Muscle 3,0.1MPa Muscle 3,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,0.1MPa_Muscle_3_1.fq.gz 0.1MPa_Muscle_3_2.fq.gz,fastq fastq,9351747300.0,31172491.0,0.1MPa Muscle 3 1.fq.gz,0:150 1:150,A:2463095348;C:2227208452;G:2232723071;T:2428688760;N:31669,150,150,,,2463095348,2227208452,2232723071,2428688760,31669,SRX12217974,SRS10194177,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.95643,0.95498,0.04562,0.04593,0.77916,0.77944,0.51753,0.51578,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66128,SRR15927794,SRX12217973,SRS10194176,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate2,,0.1MPa Muscle 2,,strain:9|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,0.1MPa Muscle 2,0.1MPa Muscle 2,0.1MPa Muscle 2,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,0.1MPa_Muscle_2_1.fq.gz 0.1MPa_Muscle_2_2.fq.gz,fastq fastq,11414630400.0,38048768.0,0.1MPa Muscle 2 1.fq.gz,0:150 1:150,A:2995912510;C:2724230960;G:2761157572;T:2933264368;N:64990,150,150,,,2995912510,2724230960,2761157572,2933264368,64990,SRX12217973,SRS10194176,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96128,0.96023,0.02793,0.02781,0.82029,0.82016,0.50742,0.50638,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66129,SRR15927795,SRX12217972,SRS10194175,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate1,,0.1MPa Muscle 1,,strain:8|dev stage:adult|sex:female|tissue:Muscle|treatment:control|BioSampleModel:Model organism or animal,,,,,,,,,0.1MPa Muscle 1,0.1MPa Muscle 1,0.1MPa Muscle 1,control,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,0.1MPa_Muscle_1_1.fq.gz 0.1MPa_Muscle_1_2.fq.gz,fastq fastq,15295642500.0,50985475.0,0.1MPa Muscle 1 1.fq.gz,0:150 1:150,A:3987711389;C:3692108838;G:3695351576;T:3920418318;N:52379,150,150,,,3987711389,3692108838,3695351576,3920418318,52379,SRX12217972,SRS10194175,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.95475,0.95466,0.03635,0.03693,0.7525,0.7542,0.51053,0.52086,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66136,SRR15927802,SRX12217965,SRS10194168,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate4,,9MPa Muscle 4,,strain:41|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,9MPa Muscle 4,9MPa Muscle 4,9MPa Muscle 4,9MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,9MPa_Muscle_4_1.fq.gz 9MPa_Muscle_4_2.fq.gz,fastq fastq,6353225700.0,21177419.0,9MPa Muscle 4 1.fq.gz,0:150 1:150,A:1715999863;C:1474644800;G:1480968914;T:1681582526;N:29597,150,150,,,1715999863,1474644800,1480968914,1681582526,29597,SRX12217965,SRS10194168,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96003,0.95939,0.0494,0.04931,0.82619,0.82641,0.55004,0.54769,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66138,SRR15927804,SRX12217963,SRS10194166,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate3,,9MPa Muscle 3,,strain:40|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,9MPa Muscle 3,9MPa Muscle 3,9MPa Muscle 3,9MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,9MPa_Muscle_3_1.fq.gz 9MPa_Muscle_3_2.fq.gz,fastq fastq,6304419900.0,21014733.0,9MPa Muscle 3 1.fq.gz,0:150 1:150,A:1677572487;C:1489287765;G:1486352895;T:1651179933;N:26820,150,150,,,1677572487,1489287765,1486352895,1651179933,26820,SRX12217963,SRS10194166,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96587,0.96598,0.04358,0.04311,0.81249,0.81282,0.4974,0.49616,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66139,SRR15927805,SRX12217962,SRS10194164,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate2,,9MPa Muscle 2,,strain:39|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,9MPa Muscle 2,9MPa Muscle 2,9MPa Muscle 2,9MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,9MPa_Muscle_2_1.fq.gz 9MPa_Muscle_2_2.fq.gz,fastq fastq,6331644900.0,21105483.0,9MPa Muscle 2 1.fq.gz,0:150 1:150,A:1682942200;C:1496960626;G:1494865186;T:1656847825;N:29063,150,150,,,1682942200,1496960626,1494865186,1656847825,29063,SRX12217962,SRS10194164,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96524,0.96513,0.03686,0.0365,0.80982,0.81154,0.54753,0.54898,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66140,SRR15927806,SRX12217961,SRS10194163,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate1,,9MPa Muscle 1,,strain:38|dev stage:adult|sex:female|tissue:Muscle|treatment:9MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,9MPa Muscle 1,9MPa Muscle 1,9MPa Muscle 1,9MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,9MPa_Muscle_1_1.fq.gz 9MPa_Muscle_1_2.fq.gz,fastq fastq,6396622200.0,21322074.0,9MPa Muscle 1 1.fq.gz,0:150 1:150,A:1699778864;C:1511454865;G:1511402516;T:1673956561;N:29394,150,150,,,1699778864,1511454865,1511402516,1673956561,29394,SRX12217961,SRS10194163,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96576,0.96563,0.04171,0.04097,0.79874,0.79902,0.47115,0.48566,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66153,SRR15927819,SRX12217948,SRS10194150,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate4,,5MPa Muscle 4,,strain:26|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,5MPa Muscle 4,5MPa Muscle 4,5MPa Muscle 4,5MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,5MPa_Muscle_4_1.fq.gz 5MPa_Muscle_4_2.fq.gz,fastq fastq,6224364000.0,20747880.0,5MPa Muscle 4 1.fq.gz,0:150 1:150,A:1641927719;C:1481415127;G:1477217131;T:1623764097;N:39926,150,150,,,1641927719,1481415127,1477217131,1623764097,39926,SRX12217948,SRS10194150,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96359,0.96348,0.04081,0.04097,0.81186,0.81189,0.48228,0.48384,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66154,SRR15927820,SRX12217947,SRS10194149,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate3,,5MPa Muscle 3,,strain:25|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,5MPa Muscle 3,5MPa Muscle 3,5MPa Muscle 3,5MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,5MPa_Muscle_3_1.fq.gz 5MPa_Muscle_3_2.fq.gz,fastq fastq,6380934000.0,21269780.0,5MPa Muscle 3 1.fq.gz,0:150 1:150,A:1671974932;C:1532410091;G:1533693387;T:1642826090;N:29500,150,150,,,1671974932,1532410091,1533693387,1642826090,29500,SRX12217947,SRS10194149,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.96596,0.96544,0.04245,0.04209,0.81168,0.81345,0.52945,0.5252,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66155,SRR15927821,SRX12217946,SRS10194148,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate2,,5MPa Muscle 2,,strain:24|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,5MPa Muscle 2,5MPa Muscle 2,5MPa Muscle 2,5MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,5MPa_Muscle_2_1.fq.gz 5MPa_Muscle_2_2.fq.gz,fastq fastq,6652238100.0,22174127.0,5MPa Muscle 2 1.fq.gz,0:150 1:150,A:1777745705;C:1559981557;G:1555946388;T:1758533051;N:31399,150,150,,,1777745705,1559981557,1555946388,1758533051,31399,SRX12217946,SRS10194148,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.95179,0.95144,0.05408,0.05364,0.71062,0.71127,0.52567,0.53034,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 66156,SRR15927822,SRX12217945,SRS10194147,SRP337553,PRJNA764015,Short Term High Hydrostatic Pressure Responses at Gene Expression Level in Zebrafish,PRJNA764015,Other,the RNA seq data of four tissues of zebrafish treated by high hydrostatic pressure,,,replicate1,,5MPa Muscle 1,,strain:23|dev stage:adult|sex:female|tissue:Muscle|treatment:5MPa4h|BioSampleModel:Model organism or animal,,,,,,,,,5MPa Muscle 1,5MPa Muscle 1,5MPa Muscle 1,5MPa4h,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP337553,,,5MPa_Muscle_1_1.fq.gz 5MPa_Muscle_1_2.fq.gz,fastq fastq,6347703000.0,21159010.0,5MPa Muscle 1 1.fq.gz,0:150 1:150,A:1667447477;C:1517500269;G:1513605953;T:1649119009;N:30292,150,150,,,1667447477,1517500269,1513605953,1649119009,30292,SRX12217945,SRS10194147,SRA1295954,Northwestern Polytechnical University|School of Ecology and Environment,Northwestern Polytechnical University,2,0.95624,0.95584,0.04626,0.04677,0.7413,0.74294,0.52854,0.52337,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-09-17,Adult,Adult,Muscle,Muscular System 70803,SRR20651070,SRX16674147,SRS14305696,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klhl40a KO4,klhl40a Mutant 4,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO4,klhl40a4,klhl40a4,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO4_1.fq.gz KO4_2.fq.gz,fastq fastq,6711352800.0,22371176.0,KO4 1.fq.gz,0:150 1:150,A:1777166363;C:1589553466;G:1610514347;T:1734012530;N:106094,150,150,,,1777166363,1589553466,1610514347,1734012530,106094,SRX16674147,SRS14305696,,,Brigham and Women's Hospital,2,0.96541,0.96534,0.04564,0.04561,0.80478,0.80594,0.49645,0.49712,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70804,SRR20651071,SRX16674146,SRS14305695,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klhl40a KO3,klhl40a Mutant 3,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO3,klhl40a3,klhl40a3,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO3_1.fq.gz KO3_2.fq.gz,fastq fastq,6837271200.0,22790904.0,KO3 1.fq.gz,0:150 1:150,A:1889665334;C:1538962427;G:1555674788;T:1852860913;N:107738,150,150,,,1889665334,1538962427,1555674788,1852860913,107738,SRX16674146,SRS14305695,,,Brigham and Women's Hospital,2,0.9394,0.93825,0.07858,0.07822,0.7413,0.74186,0.50534,0.49292,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70805,SRR20651072,SRX16674145,SRS14305694,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klhl40a KO2,klhl40a Mutant 2,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO2,klhl40a2,klhl40a2,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO2_1.fq.gz KO2_2.fq.gz,fastq fastq,6551044800.0,21836816.0,KO2 1.fq.gz,0:150 1:150,A:1793351007;C:1490899611;G:1511714794;T:1754976004;N:103384,150,150,,,1793351007,1490899611,1511714794,1754976004,103384,SRX16674145,SRS14305694,,,Brigham and Women's Hospital,2,0.95416,0.953,0.06534,0.06511,0.76678,0.76668,0.51901,0.49628,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70806,SRR20651073,SRX16674144,SRS14305693,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,klh40a KO1,klhl40a Mutant 1,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:klhl40a|phenotype:Nemaline Myopathy|BioSampleModel:Model organism or animal,,,,,,,,,KO1,klhl40a1,klhl40a1,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,KO1_1.fq.gz KO1_2.fq.gz,fastq fastq,7080009000.0,23600030.0,KO1 1.fq.gz,0:150 1:150,A:1927450674;C:1619718617;G:1639235237;T:1893497462;N:107010,150,150,,,1927450674,1619718617,1639235237,1893497462,107010,SRX16674144,SRS14305693,,,Brigham and Women's Hospital,2,0.94175,0.94193,0.06579,0.06628,0.75045,0.7503,0.49508,0.50075,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70807,SRR20651074,SRX16674143,SRS14305692,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT4,Wild type Control4,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT4,WT4,WT4,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT4_1.fq.gz WT4_2.fq.gz,fastq fastq,7079022600.0,23596742.0,WT4 1.fq.gz,0:150 1:150,A:1901387601;C:1651068590;G:1657216811;T:1869243020;N:106578,150,150,,,1901387601,1651068590,1657216811,1869243020,106578,SRX16674143,SRS14305692,,,Brigham and Women's Hospital,2,0.95455,0.95486,0.07809,0.07798,0.75491,0.75442,0.49622,0.50833,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70808,SRR20651075,SRX16674142,SRS14305691,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT3,Wild type Control3,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT3,WT3,WT3,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT3_1.fq.gz WT3_2.fq.gz,fastq fastq,6750141600.0,22500472.0,WT3 1.fq.gz,0:150 1:150,A:1809694888;C:1570721302;G:1597114393;T:1772508410;N:102607,150,150,,,1809694888,1570721302,1597114393,1772508410,102607,SRX16674142,SRS14305691,,,Brigham and Women's Hospital,2,0.95657,0.95647,0.06172,0.06163,0.76252,0.76366,0.49411,0.49204,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70809,SRR20651076,SRX16674141,SRS14305690,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT2,Wild type Control2,,strain:TU|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:3 Months|dev stage:Adult|sex:not collected|tissue:Skeletal Muscle|disease:Nemaline Myopathy|disease stg:Disease onset|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT2,WT2,WT2,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,6786893400.0,22622978.0,WT2 1.fq.gz,0:150 1:150,A:1835782156;C:1564402670;G:1586345899;T:1800260025;N:102650,150,150,,,1835782156,1564402670,1586345899,1800260025,102650,SRX16674141,SRS14305690,,,Brigham and Women's Hospital,2,0.95057,0.9495,0.06714,0.06726,0.75266,0.75333,0.50647,0.50457,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System 70810,SRR20651077,SRX16674140,SRS14305689,SRP388214,PRJNA861969,RNA seq in KLHL40 KO zebrafish muscle,PRJNA861969,Other,Mutations in KLHL40 gene results in nemaline myopathy in affected patients. To identify the contribution of transcriptome on disease pathology bulk RNA sequencing was performed in Control and KLHL40 knockout zebrafish at the onset of disease pathology at 3 month of age.,,,,WT1,Wild type Control1,,strain:AB|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 Months|dev stage:Adult|sex:male|tissue:Skeletal Muscle|disease:Nemaline Myopathy|genotype:WT|phenotype:Normal|BioSampleModel:Model organism or animal,,,,,,,,,WT1,WT1,WT1,A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA. First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150200 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptorligated cDNA at 37 C for 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot HS Illumina according to the manufacturers instructions. post cluster generation the library preparations were sequenced on an Illumina platform and paired end reads were generated.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP388214,,,WT1_1.fq.gz WT1_2.fq.gz,fastq fastq,6946359900.0,23154533.0,WT1 1.fq.gz,0:150 1:150,A:1891340276;C:1588097676;G:1606011156;T:1860805584;N:105208,150,150,,,1891340276,1588097676,1606011156,1860805584,105208,SRX16674140,SRS14305689,,,Brigham and Women's Hospital,2,0.94444,0.94509,0.07758,0.07756,0.72943,0.72878,0.50732,0.50723,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,nebnext,bulk,bulk,bulk,,United States,2022-07-26,Adult,Adult,Muscle,Muscular System