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 41404,SRR4423134,SRX2245318,SRS1745863,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 10 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 16 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: prim 16 stage31 hpf,347 10,347 10,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S10large.fastq,fastq,641713718.0,5457079.0,S10large.fastq,0:117.59,A:150550840;C:168565594;G:198254445;T:124342839;N:0,117,,,,150550840,168565594,198254445,124342839,0,SRX2245318,SRS1745863,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.94199,,0.27559,,0.93772,,0.79623,,104,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 41405,SRR4423133,SRX2245317,SRS1745862,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 9 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 5 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: prim 5 stage24 hpf,347 9,347 9,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S09large.fastq,fastq,583272900.0,4872369.0,S09large.fastq,0:119.71,A:133536706;C:155614585;G:187341444;T:106780165;N:0,119,,,,133536706,155614585,187341444,106780165,0,SRX2245317,SRS1745862,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.96394,,0.25145,,0.95785,,0.77358,,147,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 41406,SRR4423130,SRX2245314,SRS1745863,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 10 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 16 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: prim 16 stage31 hpf,348 10,348 10,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S10small.fastq,fastq,427409571.0,5026564.0,S10small.fastq,0:85.03,A:98026046;C:116630773;G:114413502;T:98339250;N:0,85,,,,98026046,116630773,114413502,98339250,0,SRX2245314,SRS1745863,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.81583,,0.17938,,0.9094,,0.63072,,126,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 41407,SRR4423129,SRX2245313,SRS1745862,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 9 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 5 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: prim 5 stage24 hpf,348 9,348 9,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S09small.fastq,fastq,516614705.0,6246071.0,S09small.fastq,0:82.71,A:117786535;C:140799134;G:139362428;T:118666608;N:0,82,,,,117786535,140799134,139362428,118666608,0,SRX2245313,SRS1745862,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.81132,,0.18952,,0.88925,,0.69719,,17,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures 41408,SRR4423128,SRX2245312,SRS1745850,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 12 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:protruding mouth stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: protruding mouth stage72 hpf,348 12,348 12,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S12small.fastq,fastq,186817590.0,3062463.0,S12small.fastq,0:61.00,A:42863072;C:49941244;G:49513828;T:44499446;N:0,61,,,,42863072,49941244,49513828,44499446,0,SRX2245312,SRS1745850,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.77668,,0.17381,,0.8915,,0.54189,,36,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Larval,Larval,Embryo Imprecise,All anatomical structures 41409,SRR4423127,SRX2245311,SRS1745851,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 11 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:long pec stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: long pec stage48 hpf,348 11,348 11,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S11small.fastq,fastq,405003101.0,5197273.0,S11small.fastq,0:77.93,A:93494059;C:109265919;G:106696649;T:95546474;N:0,77,,,,93494059,109265919,106696649,95546474,0,SRX2245311,SRS1745851,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.78244,,0.17047,,0.93379,,0.6272,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Hatching,Embryo,Embryo Imprecise,All anatomical structures 41410,SRR4423126,SRX2245310,SRS1745848,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 8 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:22 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: 22 somite stage20 hpf,347 8,347 8,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S08large.fastq,fastq,436406791.0,4063942.0,S08large.fastq,0:107.39,A:101104674;C:116028113;G:134686941;T:84587063;N:0,107,,,,101104674,116028113,134686941,84587063,0,SRX2245310,SRS1745848,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.93717,,0.24651,,0.93933,,0.83386,,120,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 41411,SRR4423125,SRX2245309,SRS1745849,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 7 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:12 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: 12 somite stage15 hpf,347 7,347 7,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S07large.fastq,fastq,537626793.0,4843104.0,S07large.fastq,0:111.01,A:126939058;C:142383462;G:163136732;T:105167541;N:0,111,,,,126939058,142383462,163136732,105167541,0,SRX2245309,SRS1745849,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.9417,,0.29157,,0.93488,,0.84573,,122,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 41412,SRR4423124,SRX2245308,SRS1745856,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 6 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:4 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: 4 somite stage11.3 hpf,347 6,347 6,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S06large.fastq,fastq,442838850.0,4133196.0,S06large.fastq,0:107.14,A:102648557;C:119062787;G:133773678;T:87353828;N:0,107,,,,102648557,119062787,133773678,87353828,0,SRX2245308,SRS1745856,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.92856,,0.24819,,0.92622,,0.85191,,53,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-14,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 41413,SRR4423123,SRX2245307,SRS1745857,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 5 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:90% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: 90% epiboly stage 9 hpf,347 5,347 5,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S05large.fastq,fastq,543194698.0,4904291.0,S05large.fastq,0:110.76,A:121453575;C:151300395;G:154852537;T:115588191;N:0,110,,,,121453575,151300395,154852537,115588191,0,SRX2245307,SRS1745857,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.91124,,0.15426,,0.92376,,0.7134,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 41414,SRR4423122,SRX2245306,SRS1745855,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 4 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:70% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: 70% epiboly stage7 hpf,347 4,347 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S04large.fastq,fastq,510714551.0,4424058.0,S04large.fastq,0:115.44,A:118836759;C:137564730;G:154371968;T:99941094;N:0,115,,,,118836759,137564730,154371968,99941094,0,SRX2245306,SRS1745855,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.94415,,0.2715,,0.93324,,0.84886,,180,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 41415,SRR4423121,SRX2245305,SRS1745854,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 3 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:zfs:0000015 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf,347 3,347 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S03large.fastq,fastq,615798661.0,4903481.0,S03large.fastq,0:125.58,A:142134014;C:166761818;G:191551564;T:115351265;N:0,125,,,,142134014,166761818,191551564,115351265,0,SRX2245305,SRS1745854,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.93992,,0.29626,,0.95408,,0.89833,,91,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures 41416,SRR4423120,SRX2245304,SRS1745852,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 2 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:high stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: high stage3.3 hpf,347 2,347 2,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S02large.fastq,fastq,399030043.0,3512248.0,S02large.fastq,0:113.61,A:91615111;C:108172506;G:123312384;T:75930042;N:0,113,,,,91615111,108172506,123312384,75930042,0,SRX2245304,SRS1745852,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.92466,,0.24175,,0.94197,,0.89366,,92,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures 41417,SRR4423119,SRX2245303,SRS1745853,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 1 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:64 cells|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: 64 cells2 hpf,347 1,347 1,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S01large.fastq,fastq,406838773.0,3451573.0,S01large.fastq,0:117.87,A:90440106;C:114282886;G:115318720;T:86797061;N:0,117,,,,90440106,114282886,115318720,86797061,0,SRX2245303,SRS1745853,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.9203,,0.10547,,0.93095,,0.75003,,158,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 41428,SRR4423108,SRX2245292,SRS1745857,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 5 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:90% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: 90% epiboly stage 9 hpf,348 5,348 5,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S05small.fastq,fastq,412237561.0,3386443.0,S05small.fastq,0:121.73,A:91644321;C:118905395;G:115070912;T:86616933;N:0,121,,,,91644321,118905395,115070912,86616933,0,SRX2245292,SRS1745857,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.81233,,0.06309,,0.93385,,0.93973,,163,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 41429,SRR4423107,SRX2245291,SRS1745856,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 6 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:4 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: 4 somite stage11.3 hpf,348 6,348 6,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S06small.fastq,fastq,535288776.0,4443685.0,S06small.fastq,0:120.46,A:119322177;C:152704452;G:149509408;T:113752739;N:0,120,,,,119322177,152704452,149509408,113752739,0,SRX2245291,SRS1745856,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.82872,,0.09035,,0.93194,,0.81296,,159,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 41430,SRR4423106,SRX2245290,SRS1745854,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 3 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:zfs:0000015 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf,348 3,348 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S03small.fastq,fastq,1025732824.0,7452991.0,S03small.fastq,0:137.63,A:225573059;C:298586545;G:288470386;T:213102834;N:0,137,,,,225573059,298586545,288470386,213102834,0,SRX2245290,SRS1745854,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.8983,,0.04271,,0.95546,,0.91281,,159,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures 41431,SRR4423105,SRX2245289,SRS1745855,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 4 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:70% epiboly stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: 70% epiboly stage7 hpf,348 4,348 4,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S04small.fastq,fastq,193259658.0,1840126.0,S04small.fastq,0:105.03,A:43516548;C:54669405;G:53501927;T:41571778;N:0,105,,,,43516548,54669405,53501927,41571778,0,SRX2245289,SRS1745855,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.81053,,0.16265,,0.90698,,0.92112,,159,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 41432,SRR4423104,SRX2245288,SRS1745853,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 1 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:64 cells|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: 64 cells2 hpf,348 1,348 1,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S01small.fastq,fastq,91910627.0,1396009.0,S01small.fastq,0:65.84,A:21663404;C:25661192;G:25069267;T:19516764;N:0,65,,,,21663404,25661192,25069267,19516764,0,SRX2245288,SRS1745853,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.56828,,0.1715,,0.92435,,0.90047,,34,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 41433,SRR4423103,SRX2245287,SRS1745852,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 2 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:high stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: high stage3.3 hpf,348 2,348 2,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S02small.fastq,fastq,304535574.0,3376105.0,S02small.fastq,0:90.20,A:69193719;C:84372087;G:86707481;T:64262287;N:0,90,,,,69193719,84372087,86707481,64262287,0,SRX2245287,SRS1745852,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.56812,,0.09695,,0.93474,,0.93654,,51,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Blastula,Embryo,Embryo Imprecise,All anatomical structures 41434,SRR4423102,SRX2245286,SRS1745851,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 11 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:long pec stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: long pec stage48 hpf,347 11,347 11,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S11large.fastq,fastq,535498199.0,5737354.0,S11large.fastq,0:93.34,A:121755741;C:143034204;G:168067337;T:102640917;N:0,93,,,,121755741,143034204,168067337,102640917,0,SRX2245286,SRS1745851,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.9065,,0.26226,,0.9388,,0.73978,,95,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Hatching,Embryo,Embryo Imprecise,All anatomical structures 41435,SRR4423101,SRX2245285,SRS1745850,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 12 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:protruding mouth stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: protruding mouth stage72 hpf,347 12,347 12,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S12large.fastq,fastq,2735647095.0,28978873.0,S12large.fastq,0:94.40,A:650857562;C:721265476;G:776126849;T:587397208;N:0,94,,,,650857562,721265476,776126849,587397208,0,SRX2245285,SRS1745850,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.87809,,0.18943,,0.88797,,0.71439,,27,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Larval,Larval,Embryo Imprecise,All anatomical structures 41436,SRR4423100,SRX2245284,SRS1745849,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 7 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:12 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: 12 somite stage15 hpf,348 7,348 7,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S07small.fastq,fastq,279201769.0,2713759.0,S07small.fastq,0:102.88,A:61655863;C:78667355;G:77702440;T:61176111;N:0,102,,,,61655863,78667355,77702440,61176111,0,SRX2245284,SRS1745849,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.79087,,0.10046,,0.89221,,0.77892,,158,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 41437,SRR4423099,SRX2245283,SRS1745848,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Time course 8 Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:22 somite stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: 22 somite stage20 hpf,348 8,348 8,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,S08small.fastq,fastq,520785540.0,4495080.0,S08small.fastq,0:115.86,A:115224831;C:149325753;G:144978190;T:111256766;N:0,115,,,,115224831,149325753,144978190,111256766,0,SRX2245283,SRS1745848,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.83781,,0.08976,,0.92904,,0.80492,,183,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 62959,SRR13520382,SRX9931400,SRS8106885,SRP303129,PRJNA694577,Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes,GSE165422,Transcriptome Analysis,Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group,,pubmed:35690839,,G8 12: pEGFP N1 injected at 12hpf,GSM5033117,,source name:zebrafish embryos|strain:TU|developmental stage:12hpf|tissue:embryo,G8 12: pEGFP N1 injected at 12hpf,Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample,zebrafish embryos,In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,,strain:TU|developmental stage:12hpf|tissue:embryo,GSM5033117,GSM5033117: G8 12: pEGFP N1 injected at 12hpf; Danio rerio; RNA Seq,GSM5033117,,1,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,GEO Accession:GSM5033117,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP303129,,,G8-12.fastq.gz,fastq,2163053937.0,12776614.0,GSM5033117 r1,0:169.30,A:581602408;C:540446105;G:566494100;T:474511324;N:0,169,,,,581602408,540446105,566494100,474511324,0,SRX9931400,SRS8106885,SRA1187495,GEO,Qingshun Zhao,1,0.73901,,0.01942,,0.7726,,0.47694,,169,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2021-01-25,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 62960,SRR13520381,SRX9931399,SRS8106884,SRP303129,PRJNA694577,Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes,GSE165422,Transcriptome Analysis,Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group,,pubmed:35690839,,G8 6: pEGFP N1 injected at 6pf,GSM5033116,,source name:zebrafish embryos|strain:TU|developmental stage:6pf|tissue:embryo,G8 6: pEGFP N1 injected at 6pf,Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample,zebrafish embryos,In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,,strain:TU|developmental stage:6pf|tissue:embryo,GSM5033116,GSM5033116: G8 6: pEGFP N1 injected at 6pf; Danio rerio; RNA Seq,GSM5033116,,1,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,GEO Accession:GSM5033116,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP303129,,,G8-6.fastq.gz,fastq,2116443238.0,12869630.0,GSM5033116 r1,0:164.45,A:580007846;C:516340658;G:549230787;T:470863947;N:0,164,,,,580007846,516340658,549230787,470863947,0,SRX9931399,SRS8106884,SRA1187495,GEO,Qingshun Zhao,1,0.73674,,0.02266,,0.79722,,0.49168,,119,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2021-01-25,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures 62961,SRR13520380,SRX9931398,SRS8106883,SRP303129,PRJNA694577,Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes,GSE165422,Transcriptome Analysis,Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group,,pubmed:35690839,,G8 1: pEGFP N1 injected at 1hpf,GSM5033115,,source name:zebrafish embryos|strain:TU|developmental stage:1hpf|tissue:embryo,G8 1: pEGFP N1 injected at 1hpf,Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample,zebrafish embryos,In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,,strain:TU|developmental stage:1hpf|tissue:embryo,GSM5033115,GSM5033115: G8 1: pEGFP N1 injected at 1hpf; Danio rerio; RNA Seq,GSM5033115,,1,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,GEO Accession:GSM5033115,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP303129,,,G8-1.fastq.gz,fastq,2029634086.0,12394054.0,GSM5033115 r1,0:163.76,A:548662597;C:501840467;G:525047427;T:454083595;N:0,163,,,,548662597,501840467,525047427,454083595,0,SRX9931398,SRS8106883,SRA1187495,GEO,Qingshun Zhao,1,0.81344,,0.01015,,0.78058,,0.48067,,90,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2021-01-25,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 62962,SRR13520379,SRX9931397,SRS8106882,SRP303129,PRJNA694577,Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes,GSE165422,Transcriptome Analysis,Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group,,pubmed:35690839,,C12: un injected at 12hpf,GSM5033114,,source name:zebrafish embryos|strain:TU|developmental stage:12hpf|tissue:embryo,C12: un injected at 12hpf,Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample,zebrafish embryos,In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,,strain:TU|developmental stage:12hpf|tissue:embryo,GSM5033114,GSM5033114: C12: un injected at 12hpf; Danio rerio; RNA Seq,GSM5033114,,1,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,GEO Accession:GSM5033114,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP303129,,,C12.fastq.gz,fastq,2287177824.0,14569411.0,GSM5033114 r1,0:156.98,A:618744606;C:567027488;G:600125143;T:501280587;N:0,156,,,,618744606,567027488,600125143,501280587,0,SRX9931397,SRS8106882,SRA1187495,GEO,Qingshun Zhao,1,0.74656,,0.02098,,0.76928,,0.47392,,184,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2021-01-25,Segmentation,Embryo,Embryo Imprecise,All anatomical structures 62963,SRR13520378,SRX9931396,SRS8106881,SRP303129,PRJNA694577,Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes,GSE165422,Transcriptome Analysis,Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group,,pubmed:35690839,,C6: un injected at 6pf,GSM5033113,,source name:zebrafish embryos|strain:TU|developmental stage:6pf|tissue:embryo,C6: un injected at 6pf,Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample,zebrafish embryos,In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,,strain:TU|developmental stage:6pf|tissue:embryo,GSM5033113,GSM5033113: C6: un injected at 6pf; Danio rerio; RNA Seq,GSM5033113,,1,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,GEO Accession:GSM5033113,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP303129,,,C6.fastq.gz,fastq,1998132252.0,12473595.0,GSM5033113 r1,0:160.19,A:548408269;C:485097126;G:517913632;T:446713225;N:0,160,,,,548408269,485097126,517913632,446713225,0,SRX9931396,SRS8106881,SRA1187495,GEO,Qingshun Zhao,1,0.73967,,0.02632,,0.79482,,0.48895,,160,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2021-01-25,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures 62964,SRR13520377,SRX9931395,SRS8106880,SRP303129,PRJNA694577,Next Generation Sequencing Facilitates Quantitative Analysis of different developmental stage pEGFP N1 injected zebrafish embryos and untreated group transcriptomes,GSE165422,Transcriptome Analysis,Purpose: Next generation sequencing NGS has revolutionized systems based analysis of cellular pathways. The goals of this study are to compare the early stage of pEGFP N1 injected zebrafish embros transcriptome profiling RNA seq to microarray and quantitative reverse transcription polymerase chain reaction qRT–PCR methods and to evaluate protocols for optimal high throughput data analysis Methods: we injected the plasmid pEGFP N1 into zebrafish zygotes by microinjection and then when the embryos to develop ttwo xxx hpf 6 hpf and 12 hpf these groups was collected respectively by deep sequencing in triplicate using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner BWA followed by ANOVA ANOVA and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Bioinformatics analysis of the transcriptome sequencing found that the expression levels of genes related to the apoptosis process Fig.1A endogenous immune response and tumor necrosis factor mediated signaling pathways were abnormal up regulation mainly including isg15 foxo3b phlda3 cdkn1a zgc:136826 and si:dkey 204l11.1 compared with the non injected group at xxxhpf. These genes are found in somatic cells to deal with foreign plasmids invasion. Overall design: Zebrafish embryos in 1hpf 6hpf and 12hpf mRNA profiles of pEGFP N1 injected and untreated group,,pubmed:35690839,,C1: un injected at 1hpf,GSM5033112,,source name:zebrafish embryos|strain:TU|developmental stage:1hpf|tissue:embryo,C1: un injected at 1hpf,Reads filtering under criteria removing reads with 20% of the base quality lower than 13 Clean Reads mapped to GRCz10 genome using Mapsplice v2.1.8 with parameters s 22 p 15 ins 6 del 6 non canonical bam o count counting Genome build: GRCz10 Supplementary files format and content: TXT file contain counts for each sample,zebrafish embryos,In the 1 cell stage of zebrafish embryos 8ng/μL pEGFP N1 was injected and the embryos of the injected group and the non injected group were collected when the embryos developed ttwo xxxhpf 6hpf and 12hpf. Add 1mL TRIzol Invitrogen USA store at 80℃,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,,strain:TU|developmental stage:1hpf|tissue:embryo,GSM5033112,GSM5033112: C1: un injected at 1hpf; Danio rerio; RNA Seq,GSM5033112,,1,RNA was harvested using Trizol reagent Invitrogen. RNA library using standard Ion proton RNA Seq Kit v2.0 protocol,GEO Accession:GSM5033112,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP303129,,,C1.fastq.gz,fastq,2073298475.0,13102880.0,GSM5033112 r1,0:158.23,A:558146987;C:513562209;G:538130597;T:463458682;N:0,158,,,,558146987,513562209,538130597,463458682,0,SRX9931395,SRS8106880,SRA1187495,GEO,Qingshun Zhao,1,0.83706,,0.01172,,0.77948,,0.48172,,233,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2021-01-25,Cleavage,Embryo,Embryo Imprecise,All anatomical structures 75396,SRR24497420,SRX20282374,SRS17609397,SRP436940,PRJNA971233,MCPIP1 functions as a safeguard of early embryonic development,GSE232220,Transcriptome Analysis,Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.,,pubmed:37805647,,Mcpip1 DN replicate3,GSM7321058,,source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing,Mcpip1 DN replicate3,Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700 using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count,embryo 6 hpf,Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.,tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N,GSM7321058,GSM7321058: Mcpip1 DN replicate3; Danio rerio; RNA Seq,GSM7321058 r1,GSM7321058,1,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP436940,,,DN_C24.fastq.gz,fastq,4215951250.0,27509986.0,GSM7321058 r1,0:153.25,A:1174686445;C:999279135;G:1076390086;T:965595584;N:0,153,,,,1174686445,999279135,1076390086,965595584,0,SRX20282374,SRS17609397,SRA1636184,"Genetics, Maria Sklodowska-Curie National Research Institute of Oncology","Genetics, Maria Skłodowska-Curie National Research Institute of Oncology",1,0.7271,,0.04079,,0.77583,,0.48331,,128,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Poland,2023-05-10,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 75397,SRR24497423,SRX20282373,SRS17609396,SRP436940,PRJNA971233,MCPIP1 functions as a safeguard of early embryonic development,GSE232220,Transcriptome Analysis,Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.,,pubmed:37805647,,Mcpip1 DN replicate2,GSM7321057,,source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing,Mcpip1 DN replicate2,Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700 using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count,embryo 6 hpf,Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.,tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N,GSM7321057,GSM7321057: Mcpip1 DN replicate2; Danio rerio; RNA Seq,GSM7321057 r1,GSM7321057,1,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP436940,,,DN_B16.fastq.gz,fastq,4150646040.0,29771678.0,GSM7321057 r1,0:139.42,A:1158168842;C:981804106;G:1077873702;T:932799390;N:0,139,,,,1158168842,981804106,1077873702,932799390,0,SRX20282373,SRS17609396,SRA1636184,"Genetics, Maria Sklodowska-Curie National Research Institute of Oncology","Genetics, Maria Skłodowska-Curie National Research Institute of Oncology",1,0.83432,,0.03292,,0.77068,,0.48489,,149,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Poland,2023-05-10,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 75398,SRR24497421,SRX20282372,SRS17609394,SRP436940,PRJNA971233,MCPIP1 functions as a safeguard of early embryonic development,GSE232220,Transcriptome Analysis,Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.,,pubmed:37805647,,Mcpip1 DN replicate1,GSM7321056,,source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N|geo loc name:missing|collection date:missing,Mcpip1 DN replicate1,Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700 using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count,embryo 6 hpf,Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.,tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1 D112N,GSM7321056,GSM7321056: Mcpip1 DN replicate1; Danio rerio; RNA Seq,GSM7321056 r1,GSM7321056,1,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP436940,,,DN_A8.fastq.gz,fastq,3405374389.0,22617333.0,GSM7321056 r1,0:150.56,A:943415180;C:825787941;G:885910600;T:750260668;N:0,150,,,,943415180,825787941,885910600,750260668,0,SRX20282372,SRS17609394,SRA1636184,"Genetics, Maria Sklodowska-Curie National Research Institute of Oncology","Genetics, Maria Skłodowska-Curie National Research Institute of Oncology",1,0.85916,,0.04442,,0.78344,,0.48648,,177,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Poland,2023-05-10,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 75399,SRR24497422,SRX20282371,SRS17609395,SRP436940,PRJNA971233,MCPIP1 functions as a safeguard of early embryonic development,GSE232220,Transcriptome Analysis,Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.,,pubmed:37805647,,Mcpip1 WT replicate3,GSM7321055,,source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing,Mcpip1 WT replicate3,Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700 using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count,embryo 6 hpf,Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.,tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1,GSM7321055,GSM7321055: Mcpip1 WT replicate3; Danio rerio; RNA Seq,GSM7321055 r1,GSM7321055,1,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP436940,,,WT_C23.fastq.gz,fastq,3644157793.0,27473010.0,GSM7321055 r1,0:132.65,A:1014320322;C:878841963;G:948316248;T:802679260;N:0,132,,,,1014320322,878841963,948316248,802679260,0,SRX20282371,SRS17609395,SRA1636184,"Genetics, Maria Sklodowska-Curie National Research Institute of Oncology","Genetics, Maria Skłodowska-Curie National Research Institute of Oncology",1,0.88531,,0.03151,,0.75101,,0.49337,,123,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Poland,2023-05-10,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 75400,SRR24497424,SRX20282370,SRS17609393,SRP436940,PRJNA971233,MCPIP1 functions as a safeguard of early embryonic development,GSE232220,Transcriptome Analysis,Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.,,pubmed:37805647,,Mcpip1 WT replicate2,GSM7321054,,source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing,Mcpip1 WT replicate2,Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700 using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count,embryo 6 hpf,Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.,tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1,GSM7321054,GSM7321054: Mcpip1 WT replicate2; Danio rerio; RNA Seq,GSM7321054 r1,GSM7321054,1,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP436940,,,WT_B15.fastq.gz,fastq,4930632556.0,30493682.0,GSM7321054 r1,0:161.69,A:1385638764;C:1206486517;G:1269832302;T:1068674973;N:0,161,,,,1385638764,1206486517,1269832302,1068674973,0,SRX20282370,SRS17609393,SRA1636184,"Genetics, Maria Sklodowska-Curie National Research Institute of Oncology","Genetics, Maria Skłodowska-Curie National Research Institute of Oncology",1,0.86405,,0.03935,,0.78324,,0.49971,,107,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Poland,2023-05-10,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures 75401,SRR24497425,SRX20282369,SRS17609392,SRP436940,PRJNA971233,MCPIP1 functions as a safeguard of early embryonic development,GSE232220,Transcriptome Analysis,Expression of zc3h12a encoding Mcpip1 is tightly controlled within first cell divisions of zebrafish. Overexpression of Mcpip1 leads to the profound transcriptomic changes in the developing embryos and impairs early embryonic development of zebrafish. Overall design: RNA seq was performed to analyse transcriptome of zebrafish embryos overexpressing Mcpip1 wild type and catalytically inactive mutant.,,pubmed:37805647,,Mcpip1 WT replicate1,GSM7321053,,source name:embryo 6 hpf|tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1|geo loc name:missing|collection date:missing,Mcpip1 WT replicate1,Signal processing and basecalling was performed with Torrent Suite version 5.14.0. Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR version 2.7.10a PMID: 23104886 and bowtie2 version 2.4.4 PMID: 22388286 for unmapped reads. Gene counts were created with htseq count PMID: 25260700 using Ensembl gene model. Differential expression was tested with DESeq2 version version 1.40.1 PMID: 2551628 Assembly: Danio rerio Ensembl genome version GRCz11 Supplementary files format and content: DESeq2 normalized count,embryo 6 hpf,Zebrafish eggs at 1 cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.,tissue:embryo 6 hpf|genotype:AB/TL|treatment:microinjection with mRNA encoding zebrafish Mcpip1,GSM7321053,GSM7321053: Mcpip1 WT replicate1; Danio rerio; RNA Seq,GSM7321053 r1,GSM7321053,1,Zebrafish embryos were collected in Fenozol A&A Biotechnology Gdansk Polska and stored at 80°C prior to analysis. For RNA isolation the samples were homogenized in Fenozol using a tissue homogenizer OMNI International Kennesaw GA USA. The poly A mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit Thermo. The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA Seq Kit v2 Thermo. The libraries were generated from 1 15 ng of mRNA by fragmenting the mRNA with RNaseIII purifying the fragmented RNA and hybridizing and ligating it with Ion adaptors. Subsequently the RNA products were reverse transcribed and amplified to double stranded cDNA and then purified using a magnetic bead based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 Agilent. Each library was diluted to 53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument Thermo using reagents from the Ion PI Hi Q 200 Kit Thermo and Ion PI v3 Proton Chip.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP436940,,,WT_A7.fastq.gz,fastq,4888312783.0,29414563.0,GSM7321053 r1,0:166.19,A:1356799075;C:1172146709;G:1273947582;T:1085419417;N:0,166,,,,1356799075,1172146709,1273947582,1085419417,0,SRX20282369,SRS17609392,SRA1636184,"Genetics, Maria Sklodowska-Curie National Research Institute of Oncology","Genetics, Maria Skłodowska-Curie National Research Institute of Oncology",1,0.82661,,0.05547,,0.7751,,0.49668,,188,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Poland,2023-05-10,Multi-stage,Multi-stage,Embryo Imprecise,All anatomical structures