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 30599,SRR27865238,SRX23527802,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con MO,6,6,con MO,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,con-KDM_1.fq.gz con-KDM_2.fq.gz,fastq fastq,7088132100.0,23627107.0,con KDM 1.fq.gz,0:150 1:150,A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033,150,150,,,1893419600,1649526065,1662549202,1882459200,178033,SRX23527802,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 30600,SRR27865239,SRX23527801,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,KDM4C MO,5,5,KDM4C MO,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,KDM-MO_1.fq.gz KDM-MO_2.fq.gz,fastq fastq,7876840500.0,26256135.0,KDM MO 1.fq.gz,0:150 1:150,A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469,150,150,,,2104173142,1831662159,1843980192,2096831538,193469,SRX23527801,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 30601,SRR27865240,SRX23527800,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,ZNF662 MO,4,4,ZNF662 MO,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,znf547-MO_1.fq.gz znf547-MO_2.fq.gz,fastq fastq,7573815300.0,25246051.0,znf547 MO 1.fq.gz,0:150 1:150,A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628,150,150,,,2014197761,1766587259,1782217029,2010540623,272628,SRX23527800,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 30602,SRR27865241,SRX23527799,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,SEMA5A RNA,3,3,SEMA5A RNA,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,semRNA_1.fq.gz semRNA_2.fq.gz,fastq fastq,5575566000.0,18585220.0,semRNA 1.fq.gz,0:150 1:150,A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165,150,150,,,1456001758,1325628099,1339796989,1454076989,62165,SRX23527799,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 30603,SRR27865242,SRX23527798,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,MT ATP6 RNA,2,2,MT ATP6 RNA,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz,fastq fastq,5437771200.0,18125904.0,ATP6 RNA 1.fq.gz,0:150 1:150,A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633,150,150,,,1438540045,1272310670,1290121053,1436739799,59633,SRX23527798,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 30604,SRR27865243,SRX23527797,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con RNA,1,1,con RNA,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,con-RNA_1.fq.gz con-RNA_2.fq.gz,fastq fastq,6733158900.0,22443863.0,con RNA 1.fq.gz,0:150 1:150,A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220,150,150,,,1766014369,1595337569,1610127771,1761604971,74220,SRX23527797,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 33326,SRR29962931,SRX25444536,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,zx150 RNAseq,4,4,zx150 RNAseq,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,zx150_input_1.fq.gz zx150_input_2.fq.gz,fastq fastq,11540682300.0,38468941.0,zx150 input 1.fq.gz,0:150 1:150,A:3038586049;C:2720235923;G:2771004747;T:3010645578;N:210003,150,150,,,3038586049,2720235923,2771004747,3010645578,210003,SRX25444536,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures 33327,SRR29962932,SRX25444535,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con RNAseq,3,3,con RNAseq,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,con-zx150_input_1.fq.gz con-zx150_input_2.fq.gz,fastq fastq,11610174300.0,38700581.0,con zx150 input 1.fq.gz,0:150 1:150,A:3049654977;C:2746004045;G:2795023766;T:3019280685;N:210827,150,150,,,3049654977,2746004045,2795023766,3019280685,210827,SRX25444535,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures 33328,SRR29962933,SRX25444534,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,zx150 m6A,2,2,zx150 m6A,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,zx150_IP_1.fq.gz zx150_IP_2.fq.gz,fastq fastq,17410816801.0,80469610.0,zx150 IP 1.fq.gz,0:108.79 1:107.58,A:4434870667;C:3759430468;G:4812205613;T:4404166470;N:143583,108,107,,,4434870667,3759430468,4812205613,4404166470,143583,SRX25444534,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures 33329,SRR29962934,SRX25444533,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con m6A,1,1,con m6A,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,con-zx150_IP_1.fq.gz con-zx150_IP_2.fq.gz,fastq fastq,16822889423.0,77865752.0,con zx150 IP 1.fq.gz,0:108.68 1:107.37,A:4324048234;C:3668630618;G:4601614069;T:4228151501;N:445001,108,107,,,4324048234,3668630618,4601614069,4228151501,445001,SRX25444533,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures 36663,SRR800049,SRX257156,SRS405710,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,sphere RNAseq 5azaCyD control,,strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere,,,,,,,,,sphere RNAseq 5azaCyD control,sphere RNAseq 5azaCyD control,9323X2,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP020008,,,sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz,Illumina native,2563410950.0,51268219.0,9323X2 120628 SN141 0513 AD12CFACXX 4,0:50,A:663337120;C:603101927;G:752336300;T:542924123;N:1711480,50,,,,663337120,603101927,752336300,542924123,1711480,SRX257156,SRS405710,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.65713,,0.09976,,0.81677,,0.81063,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-05-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures 36664,SRR800046,SRX257155,SRS405709,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,sphere RNAseq 5azaCyD treatment,,strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere,,,,,,,,,sphere RNAseq 5azaCyD treatment,sphere RNAseq 5azaCyD treatment,9323X1,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,500Application ReadForward1,SRP020008,,,sphere_RNAseq_5azaCyD_treatment_SE_9323X1_120628_SN141_0513_AD12CFACXX_4.txt.gz,Illumina native,2595654550.0,51913091.0,9323X1 120628 SN141 0513 AD12CFACXX 4,0:50,A:676999669;C:618386951;G:759497082;T:539035799;N:1735049,50,,,,676999669,618386951,759497082,539035799,1735049,SRX257155,SRS405709,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.76926,,0.12287,,0.82408,,0.72244,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-04-03,Blastula,Embryo,Embryo Imprecise,All anatomical structures 71388,SRR21528734,SRX17531094,SRS15079603,SRP396673,PRJNA879284,Toxicology evaluation of overdose hydroxychloroquine on zebrafish Danio rerio embryos,PRJNA879284,Other,,,,,HCQ embryos,HCQ embryos,,strain:AB|breed:Egg water|age:0.8year|dev stage:5hpf|sex:not applicable|tissue:embryo|cell line:embryo|cell type:embryo|collected by:Straw|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of HCQ embryo,2,2,HCQ embryo,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP396673,,,HCQ_1.fq.gz HCQ_2.fq.gz,fastq fastq,6247416600.0,20824722.0,HCQ 1.fq.gz,0:150 1:150,A:1705532494;C:1419469418;G:1445959454;T:1676101471;N:353763,150,150,,,1705532494,1419469418,1445959454,1676101471,353763,SRX17531094,SRS15079603,SRA1495070,Sichuan University|West China Second University Hospital,Sichuan University,2,0.95531,0.95352,0.05755,0.05707,0.7513,0.75215,0.48749,0.48711,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-09-12,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 71389,SRR21528735,SRX17531093,SRS15079603,SRP396673,PRJNA879284,Toxicology evaluation of overdose hydroxychloroquine on zebrafish Danio rerio embryos,PRJNA879284,Other,,,,,HCQ embryos,HCQ embryos,,strain:AB|breed:Egg water|age:0.8year|dev stage:5hpf|sex:not applicable|tissue:embryo|cell line:embryo|cell type:embryo|collected by:Straw|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of WT embryo,1,1,WT embryo,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP396673,,,HCQ-con_1.fq.gz HCQ-con_2.fq.gz,fastq fastq,6039833100.0,20132777.0,HCQ con 1.fq.gz,0:150 1:150,A:1632793916;C:1383182551;G:1413411225;T:1610087974;N:357434,150,150,,,1632793916,1383182551,1413411225,1610087974,357434,SRX17531093,SRS15079603,SRA1495070,Sichuan University|West China Second University Hospital,Sichuan University,2,0.95216,0.95061,0.05402,0.05357,0.75185,0.75262,0.48712,0.48749,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2022-09-12,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 75644,SRR24752590,SRX20528694,SRS17837826,SRP439887,PRJNA976915,Embryotoxicity evaluation of Gentamicin using the zebrafish model,PRJNA976915,Other,Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model,,,,Embryos 5hpf,Embryos 5hpf,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Embryo 5hpf Gentanicin,2,2,Embryo 5hpf Gentanicin,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP439887,,,Qingda_1.fq.gz Qingda_2.fq.gz,fastq fastq,6985244400.0,23284148.0,Qingda 1.fq.gz,0:150 1:150,A:1634658220;C:1842974934;G:1881072995;T:1626517291;N:20960,150,150,,,1634658220,1842974934,1881072995,1626517291,20960,SRX20528694,SRS17837826,SRA1645398,Sichuan University|West China Second University Hospital,Sichuan University,2,0.96818,0.97235,0.21368,0.21914,0.79265,0.79273,0.53525,0.50366,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2023-05-27,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75645,SRR24752591,SRX20528693,SRS17837826,SRP439887,PRJNA976915,Embryotoxicity evaluation of Gentamicin using the zebrafish model,PRJNA976915,Other,Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model,,,,Embryos 5hpf,Embryos 5hpf,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of WT Embryo 5hpf,1,1,WT Embryo 5hpf,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP439887,,,WT-blank_1.fq.gz WT-blank_2.fq.gz,fastq fastq,6062337300.0,20207791.0,WT blank 1.fq.gz,0:150 1:150,A:1526499059;C:1498285888;G:1526586728;T:1510947161;N:18464,150,150,,,1526499059,1498285888,1526586728,1510947161,18464,SRX20528693,SRS17837826,SRA1645398,Sichuan University|West China Second University Hospital,Sichuan University,2,0.96896,0.97182,0.02595,0.02539,0.77861,0.77865,0.48078,0.48377,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2023-05-27,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75646,SRR24754508,SRX20530612,SRS17839502,SRP439912,PRJNA976946,MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model,PRJNA976946,Other,MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model,,,,m6A Embryos 5hpf,m6A Embryos 5hpf,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal,,,,,,,,,MeRIP Seq of Embryo 5hpf Gentanicin,2,2,Embryo 5hpf Gentanicin,,,RIP-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP439912,,,QingdaIP_1.fq.gz QingdaIP_2.fq.gz Qingdainput_1.fq.gz Qingdainput_2.fq.gz,fastq fastq fastq fastq,16015155900.0,53383853.0,QingdaIP 1.fq.gz,0:150 1:150,A:3341079522;C:3427050846;G:6045646273;T:3201293287;N:85972,150,150,,,3341079522,3427050846,6045646273,3201293287,85972,SRX20530612,SRS17839502,SRA1645459,Sichuan University|West China Second University Hospital,Sichuan University,2,0.75159,0.73659,0.1359,0.13542,0.8117,0.81172,0.51543,0.51251,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2023-05-27,Blastula,Embryo,Embryo Imprecise,All anatomical structures 75647,SRR24754509,SRX20530611,SRS17839502,SRP439912,PRJNA976946,MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model,PRJNA976946,Other,MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model,,,,m6A Embryos 5hpf,m6A Embryos 5hpf,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal,,,,,,,,,MeRIP Seq of WT Embryo 5hpf,1,1,WT Embryo 5hpf,,,RIP-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP439912,,,WT-blankIP_1.fq.gz WT-blankIP_2.fq.gz WT-blankinput_1.fq.gz WT-blankinput_2.fq.gz,fastq fastq fastq fastq,15326922600.0,51089742.0,WT blankIP 1.fq.gz,0:150 1:150,A:3289509867;C:3239692571;G:5510216977;T:3287142341;N:360844,150,150,,,3289509867,3239692571,5510216977,3287142341,360844,SRX20530611,SRS17839502,SRA1645459,Sichuan University|West China Second University Hospital,Sichuan University,2,0.71182,0.69789,0.02169,0.02058,0.80409,0.80395,0.47813,0.48125,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2023-05-27,Blastula,Embryo,Embryo Imprecise,All anatomical structures 77327,SRR065197,SRX026483,SRS114570,SRP003472,PRJXX3472,RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation,ZF_U1C,Transcriptome Analysis,Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.,,pubmed:21468032,Total RNA from 3 dpf mutant zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library.,Total RNA from 3 dpf mutant zebrafish embryos,MUT,,,,,,,,,,,3 dpf mutant zebrafish embryos,MUT,mut,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer II,0Application ReadForward1,SRP003472,,,MUT_1.txt.tar.gz MUT_2N.txt.tar.gz MUT_3.txt.tar.gz,fastq fastq fastq,2418427464.0,31821414.0,MUT,0:76,A:604956506;C:600954722;G:608767958;T:600808464;N:2939814,76,,,,604956506,600954722,608767958,600808464,2939814,SRX026483,SRS114570,,,Justus-Liebig University Giessen,1,0.91109,,0.077,,0.71445,,0.44387,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,Germany,2011-03-31,Larval,Larval,Embryo Imprecise,All anatomical structures 77328,SRR065196,SRX026482,SRS114569,SRP003472,PRJXX3472,RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation,ZF_U1C,Transcriptome Analysis,Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.,,pubmed:21468032,Total RNA from 3 dpf wildtype zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library.,Total RNA from 3 dpf wildtype zebrafish embryos,WT,,,,,,,,,,,3 dpf wildtype embryos,WT,wt,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina Genome Analyzer II,0Application ReadForward1,SRP003472,,,WT_1.txt.tar WT_2.txt.tar.gz WT_3.txt.tar.gz WT_4.txt.tar.gz,fastq fastq fastq fastq,2697785376.0,35497176.0,WT,0:76,A:676186765;C:669131645;G:670872323;T:676745206;N:4849437,76,,,,676186765,669131645,670872323,676745206,4849437,SRX026482,SRS114569,,,Justus-Liebig University Giessen,1,0.9435,,0.087,,0.71429,,0.46075,,76,,B,,usable mapping rate,illumina,early_illumina,unknown,other,unknown,bulk,unknown,unknown,,Germany,2011-03-31,Larval,Larval,Embryo Imprecise,All anatomical structures