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
9775,ERR3838754,ERX3851420,ERS4266444,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 wt rep2,SAMEA6501995,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501995|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 wt rep2 p,Soma prim5 wt rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_prim5_rep2_R1.fastq.gz Somatic_prim5_rep2_R2.fastq.gz,fastq fastq,2664555542.0,17942996.0,E MTAB 8707:Somatic prim5 rep2 R,0:74.25 1:74.25,A:757990974;C:568005838;G:586848520;T:749991976;N:1718234,74,74,,,757990974,568005838,586848520,749991976,1718234,ERX3851420,ERS4266444,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92034,0.91779,0.22669,0.22761,0.74769,0.74911,0.45866,0.45282,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9776,ERR3838753,ERX3851419,ERS4266443,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 wt rep1,SAMEA6501994,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501994|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 wt rep1 p,Soma prim5 wt rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_prim5_rep1_R1.fastq.gz Somatic_prim5_rep1_R2.fastq.gz,fastq fastq,1847156504.0,12386853.0,E MTAB 8707:Somatic prim5 rep1 R,0:74.56 1:74.56,A:519724449;C:399975516;G:411702918;T:514818493;N:935128,74,74,,,519724449,399975516,411702918,514818493,935128,ERX3851419,ERS4266443,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93526,0.93319,0.24244,0.24304,0.75073,0.75201,0.44773,0.44885,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9777,ERR3838752,ERX3851418,ERS4266442,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 Morpholino rep2,SAMEA6501993,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501993|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 Morpholino rep2 p,Soma prim5 Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S14_R1.fastq.gz S14_R2.fastq.gz,fastq fastq,953947657.0,6389852.0,E MTAB 8707:S14 R,0:74.64 1:74.65,A:271485260;C:204208876;G:210319402;T:267490986;N:443133,74,74,,,271485260,204208876,210319402,267490986,443133,ERX3851418,ERS4266442,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93577,0.93619,0.1141,0.11516,0.72644,0.72892,0.4694,0.46965,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9778,ERR3838751,ERX3851417,ERS4266441,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 Morpholino rep1,SAMEA6501992,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501992|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 Morpholino rep1 p,Soma prim5 Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S12_R1.fastq.gz S12_R2.fastq.gz,fastq fastq,753719404.0,5057589.0,E MTAB 8707:S12 R,0:74.51 1:74.52,A:216097326;C:160004832;G:164724356;T:212507268;N:385622,74,74,,,216097326,160004832,164724356,212507268,385622,ERX3851417,ERS4266441,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93958,0.93943,0.10854,0.1092,0.73267,0.73663,0.45629,0.47862,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9779,ERR3838750,ERX3851416,ERS4266440,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 5mismatch Morpholino rep2,SAMEA6501991,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501991|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 5mismatch Morpholino rep2 p,Soma prim5 5mismatch Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S18_R1.fastq.gz S18_R2.fastq.gz,fastq fastq,847966718.0,5668126.0,E MTAB 8707:S18 R,0:74.80 1:74.80,A:230723434;C:191446710;G:197114792;T:228326953;N:354829,74,74,,,230723434,191446710,197114792,228326953,354829,ERX3851416,ERS4266440,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92436,0.92488,0.08973,0.09012,0.73971,0.74192,0.45291,0.45397,76,73,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9780,ERR3838749,ERX3851415,ERS4266439,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 5mismatch Morpholino rep1,SAMEA6501990,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501990|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 5mismatch Morpholino rep1 p,Soma prim5 5mismatch Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S16_R1.fastq.gz S16_R2.fastq.gz,fastq fastq,444518989.0,2971315.0,E MTAB 8707:S16 R,0:74.80 1:74.80,A:121398448;C:100282796;G:103112415;T:119559792;N:165538,74,74,,,121398448,100282796,103112415,119559792,165538,ERX3851415,ERS4266439,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92469,0.92438,0.09917,0.10006,0.72279,0.7251,0.45852,0.46016,73,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9781,ERR3838748,ERX3851414,ERS4266438,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma High rep2,SAMEA6501989,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501989|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep2|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma High rep2 p,Soma High rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Fabio_High_rep2_soma_R1.fastq.gz Fabio_High_rep2_soma_R2.fastq.gz,fastq fastq,2072343523.0,13904136.0,E MTAB 8707:Fabio High rep2 soma R,0:74.52 1:74.53,A:596021076;C:439789413;G:451992691;T:583604290;N:936053,74,74,,,596021076,439789413,451992691,583604290,936053,ERX3851414,ERS4266438,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.94263,0.94098,0.04804,0.04844,0.75797,0.76039,0.50847,0.5014,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9782,ERR3838747,ERX3851413,ERS4266437,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma High rep1,SAMEA6501988,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501988|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep1|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma High rep1 p,Soma High rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_High_rep1_R1.fastq.gz Somatic_High_rep1_R2.fastq.gz,fastq fastq,6013555644.0,40662218.0,E MTAB 8707:Somatic High rep1 R,0:73.94 1:73.95,A:1821348300;C:1185534582;G:1227848010;T:1774836657;N:3988095,73,73,,,1821348300,1185534582,1227848010,1774836657,3988095,ERX3851413,ERS4266437,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93539,0.9357,0.07066,0.07028,0.76197,0.76386,0.54301,0.54343,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9783,ERR3838746,ERX3851412,ERS4266436,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma dome rep2,SAMEA6501987,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501987|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep2|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma dome rep2 p,Soma dome rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S10_R1.fastq.gz S10_R2.fastq.gz,fastq fastq,1086124503.0,7272505.0,E MTAB 8707:S10 R,0:74.67 1:74.68,A:305920447;C:235855931;G:243442186;T:300439294;N:466645,74,74,,,305920447,235855931,243442186,300439294,466645,ERX3851412,ERS4266436,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.94089,0.94085,0.04872,0.04916,0.7419,0.74355,0.51209,0.5119,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9784,ERR3838745,ERX3851411,ERS4266435,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma dome rep1,SAMEA6501986,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501986|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep1|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma dome rep1 p,Soma dome rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S8_R1.fastq.gz S8_R2.fastq.gz,fastq fastq,336100162.0,2240589.0,E MTAB 8707:S8 R,0:75.00 1:75.00,A:93960580;C:73499585;G:75981355;T:92580945;N:77697,75,75,,,93960580,73499585,75981355,92580945,77697,ERX3851411,ERS4266435,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93874,0.93856,0.05265,0.0517,0.74188,0.74381,0.51181,0.51086,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9785,ERR3838744,ERX3851410,ERS4266434,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma 256 cell rep2,SAMEA6501985,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501985|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma 256 cell rep2 p,Soma 256 cell rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S2_R1.fastq.gz S2_R2.fastq.gz,fastq fastq,1272080863.0,8551103.0,E MTAB 8707:S2 R,0:74.38 1:74.38,A:364033393;C:268850689;G:276270908;T:362172455;N:753418,74,74,,,364033393,268850689,276270908,362172455,753418,ERX3851410,ERS4266434,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.80562,0.80436,0.23702,0.23786,0.77914,0.77991,0.51225,0.5092,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9786,ERR3838743,ERX3851409,ERS4266433,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma 256 cell rep1,SAMEA6501984,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501984|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma 256 cell rep1 p,Soma 256 cell rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_256_rep1_R1.fastq.gz Somatic_256_rep1_R2.fastq.gz,fastq fastq,2254901578.0,15144857.0,E MTAB 8707:Somatic 256 rep1 R,0:74.44 1:74.45,A:648357135;C:475813294;G:492914743;T:636658631;N:1157775,74,74,,,648357135,475813294,492914743,636658631,1157775,ERX3851409,ERS4266433,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92992,0.92787,0.07245,0.07214,0.7599,0.76084,0.53758,0.53839,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9787,ERR3838742,ERX3851408,ERS4266432,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma 10somites rep2,SAMEA6501983,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501983|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep2|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma 10somites rep2 p,Soma 10somites rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S6_R1.fastq.gz S6_R2.fastq.gz,fastq fastq,1244080980.0,8338002.0,E MTAB 8707:S6 R,0:74.60 1:74.60,A:356418931;C:263292901;G:270630630;T:353140798;N:597720,74,74,,,356418931,263292901,270630630,353140798,597720,ERX3851408,ERS4266432,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.86791,0.86732,0.20223,0.20398,0.75588,0.75883,0.4862,0.48313,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Segmentation,Embryo,Whole Organism,All anatomical structures
9788,ERR3838741,ERX3851407,ERS4266431,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma 10somites rep1,SAMEA6501982,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501982|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep1|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma 10somites rep1 p,Soma 10somites rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S4_R1.fastq.gz S4_R2.fastq.gz,fastq fastq,946153328.0,6354843.0,E MTAB 8707:S4 R,0:74.44 1:74.45,A:268310887;C:203457903;G:208969410;T:264875129;N:539999,74,74,,,268310887,203457903,208969410,264875129,539999,ERX3851407,ERS4266431,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92415,0.92372,0.12138,0.12268,0.74061,0.74422,0.47246,0.47448,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Segmentation,Embryo,Whole Organism,All anatomical structures
9789,ERR3838740,ERX3851406,ERS4266430,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 wt rep2,SAMEA6501981,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501981|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 wt rep2 p,PGC prim5 wt rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_prim5_rep2_R1.fastq.gz PGC_prim5_rep2_R2.fastq.gz,fastq fastq,2236371655.0,15023634.0,E MTAB 8707:PGC prim5 rep2 R,0:74.43 1:74.43,A:619039687;C:495191024;G:509021767;T:611885185;N:1233992,74,74,,,619039687,495191024,509021767,611885185,1233992,ERX3851406,ERS4266430,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93137,0.92838,0.23991,0.24045,0.71435,0.71591,0.49054,0.49302,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9790,ERR3838739,ERX3851405,ERS4266429,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 wt rep1,SAMEA6501980,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501980|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 wt rep1 p,PGC prim5 wt rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_prim5_rep1_R1.fastq.gz PGC_prim5_rep1_R2.fastq.gz,fastq fastq,1619398294.0,10873533.0,E MTAB 8707:PGC prim5 rep1 R,0:74.46 1:74.47,A:450612629;C:355178930;G:365650222;T:447083613;N:872900,74,74,,,450612629,355178930,365650222,447083613,872900,ERX3851405,ERS4266429,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92755,0.92901,0.22893,0.22952,0.71131,0.71372,0.49829,0.50019,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9791,ERR3838738,ERX3851404,ERS4266428,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 Morpholino rep2,SAMEA6501979,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501979|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 Morpholino rep2 p,PGC prim5 Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S13_R1.fastq.gz S13_R2.fastq.gz,fastq fastq,906443913.0,6069224.0,E MTAB 8707:S13 R,0:74.67 1:74.68,A:256935983;C:195137600;G:200975999;T:253026767;N:367564,74,74,,,256935983,195137600,200975999,253026767,367564,ERX3851404,ERS4266428,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93468,0.93605,0.09793,0.09817,0.71163,0.71291,0.48766,0.48921,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9792,ERR3838737,ERX3851403,ERS4266427,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 Morpholino rep1,SAMEA6501978,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501978|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 Morpholino rep1 p,PGC prim5 Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Fabio_cat_11_R1.fastq.gz Fabio_cat_11_R2.fastq.gz,fastq fastq,1078919524.0,7241200.0,E MTAB 8707:Fabio cat 11 R,0:74.50 1:74.50,A:308200726;C:229836659;G:236649504;T:303673221;N:559414,74,74,,,308200726,229836659,236649504,303673221,559414,ERX3851403,ERS4266427,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93808,0.93753,0.10449,0.10446,0.70733,0.71017,0.48103,0.48247,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9793,ERR3838736,ERX3851402,ERS4266426,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 5mismatch Morpholino rep2,SAMEA6501977,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501977|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 5mismatch Morpholino rep2 p,PGC prim5 5mismatch Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S17_R1.fastq.gz S17_R2.fastq.gz,fastq fastq,673911944.0,4501723.0,E MTAB 8707:S17 R,0:74.85 1:74.85,A:184466911;C:150779527;G:155693395;T:182720480;N:251631,74,74,,,184466911,150779527,155693395,182720480,251631,ERX3851402,ERS4266426,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.9199,0.92023,0.08791,0.08923,0.70132,0.70378,0.49183,0.49425,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9794,ERR3838735,ERX3851401,ERS4266425,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 5mismatch Morpholino rep1,SAMEA6501976,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501976|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 5mismatch Morpholino rep1 p,PGC prim5 5mismatch Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S15_R1.fastq.gz S15_R2.fastq.gz,fastq fastq,565636692.0,3782000.0,E MTAB 8707:S15 R,0:74.78 1:74.78,A:157353454;C:124504476;G:128260137;T:155314004;N:204621,74,74,,,157353454,124504476,128260137,155314004,204621,ERX3851401,ERS4266425,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.91956,0.91996,0.08306,0.08458,0.69982,0.70203,0.48525,0.48771,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9795,ERR3838734,ERX3851400,ERS4266424,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC High rep2,SAMEA6501975,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501975|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep2|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC High rep2 p,PGC High rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_High_rep2_R1.fastq.gz PGC_High_rep2_R2.fastq.gz,fastq fastq,2491013839.0,16740632.0,E MTAB 8707:PGC High rep2 R,0:74.40 1:74.40,A:715637079;C:527451931;G:545855323;T:700774175;N:1295331,74,74,,,715637079,527451931,545855323,700774175,1295331,ERX3851400,ERS4266424,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93381,0.93556,0.06095,0.06172,0.76094,0.76364,0.52942,0.53118,74,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9796,ERR3838733,ERX3851399,ERS4266423,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC High rep1,SAMEA6501974,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501974|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep1|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC High rep1 p,PGC High rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_High_rep1_R1.fastq.gz PGC_High_rep1_R2.fastq.gz,fastq fastq,2055218051.0,13801653.0,E MTAB 8707:PGC High rep1 R,0:74.45 1:74.46,A:594747301;C:431446277;G:445665283;T:582330624;N:1028566,74,74,,,594747301,431446277,445665283,582330624,1028566,ERX3851399,ERS4266423,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93644,0.93494,0.06937,0.07015,0.76353,0.7653,0.45909,0.44979,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9797,ERR3838732,ERX3851398,ERS4266422,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC dome rep2,SAMEA6501973,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501973|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep2|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC dome rep2 p,PGC dome rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S9_R1.fastq.gz S9_R2.fastq.gz,fastq fastq,882858901.0,5912255.0,E MTAB 8707:S9 R,0:74.66 1:74.67,A:246639630;C:193554406;G:199940889;T:242369366;N:354610,74,74,,,246639630,193554406,199940889,242369366,354610,ERX3851398,ERS4266422,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.94045,0.9404,0.04635,0.04658,0.74582,0.74777,0.4915,0.49248,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9798,ERR3838731,ERX3851397,ERS4266421,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC dome rep1,SAMEA6501972,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501972|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep1|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC dome rep1 p,PGC dome rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S7_R1.fastq.gz S7_R2.fastq.gz,fastq fastq,592299285.0,3961989.0,E MTAB 8707:S7 R,0:74.75 1:74.75,A:166664600;C:128421892;G:132787149;T:164189412;N:236232,74,74,,,166664600,128421892,132787149,164189412,236232,ERX3851397,ERS4266421,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93981,0.94032,0.04868,0.04843,0.74627,0.74722,0.49243,0.48872,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9799,ERR3838730,ERX3851396,ERS4266420,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 256 cell rep2,SAMEA6501971,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501971|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC 256 cell rep2 p,PGC 256 cell rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S1_R1.fastq.gz S1_R2.fastq.gz,fastq fastq,745277323.0,4983607.0,E MTAB 8707:S1 R,0:74.77 1:74.77,A:208352741;C:163024343;G:168234953;T:205391192;N:274094,74,74,,,208352741,163024343,168234953,205391192,274094,ERX3851396,ERS4266420,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.9393,0.9395,0.03941,0.03941,0.75473,0.75708,0.51338,0.51754,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9800,ERR3838729,ERX3851395,ERS4266419,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 256 cell rep1,SAMEA6501970,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501970|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC 256 cell rep1 p,PGC 256 cell rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_256_rep1_R1.fastq.gz PGC_256_rep1_R2.fastq.gz,fastq fastq,1876891175.0,12625794.0,E MTAB 8707:PGC 256 rep1 R,0:74.32 1:74.33,A:539140549;C:396392844;G:411568412;T:528672735;N:1116635,74,74,,,539140549,396392844,411568412,528672735,1116635,ERX3851395,ERS4266419,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92251,0.92173,0.06705,0.06723,0.76059,0.76374,0.54467,0.54135,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Blastula,Embryo,Whole Organism,All anatomical structures
9801,ERR3838728,ERX3851394,ERS4266418,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 10somites rep2,SAMEA6501969,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501969|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep2|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC 10somites rep2 p,PGC 10somites rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S5_R1.fastq.gz S5_R2.fastq.gz,fastq fastq,1186993033.0,7958634.0,E MTAB 8707:S5 R,0:74.57 1:74.58,A:332263881;C:259239478;G:267014990;T:327946611;N:528073,74,74,,,332263881,259239478,267014990,327946611,528073,ERX3851394,ERS4266418,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.90713,0.9062,0.10071,0.1016,0.73058,0.73279,0.48458,0.48038,74,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Segmentation,Embryo,Whole Organism,All anatomical structures
9802,ERR3838727,ERX3851393,ERS4266417,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 10somites rep1,SAMEA6501968,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501968|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep1|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC 10somites rep1 p,PGC 10somites rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S3_R1.fastq.gz S3_R2.fastq.gz,fastq fastq,1230551446.0,8251644.0,E MTAB 8707:S3 R,0:74.56 1:74.57,A:345409587;C:267720436;G:275626594;T:341185818;N:609011,74,74,,,345409587,267720436,275626594,341185818,609011,ERX3851393,ERS4266417,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.90983,0.90985,0.1005,0.10037,0.72622,0.72825,0.49116,0.49135,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Segmentation,Embryo,Whole Organism,All anatomical structures
10111,ERR4911024,ERX4777847,ERS5435613,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC Rescue rep2,SAMEA7678632,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678632|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep2|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC Rescue rep2 p,PGC Rescue rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_Rescue_PGC_rep2_R1.fastq.gz Tdrd7_Rescue_PGC_rep2_R2.fastq.gz,fastq fastq,6487121744.0,43103086.0,E MTAB 9857:Tdrd7 Rescue PGC rep2 R,0:75.26 1:75.24,A:1769293880;C:1469053016;G:1516553427;T:1729496045;N:2725376,75,75,,,1769293880,1469053016,1516553427,1729496045,2725376,ERX4777847,ERS5435613,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.95185,0.95349,0.04302,0.04315,0.72829,0.73022,0.47176,0.47104,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10112,ERR4911023,ERX4777846,ERS5435612,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC Rescue rep1,SAMEA7678631,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678631|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep1|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC Rescue rep1 p,PGC Rescue rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_Rescue_PGC_rep1_R1.fastq.gz Tdrd7_Rescue_PGC_rep1_R2.fastq.gz,fastq fastq,5952473889.0,39454929.0,E MTAB 9857:Tdrd7 Rescue PGC rep1 R,0:75.44 1:75.43,A:1640467527;C:1332668425;G:1380033115;T:1597665169;N:1639653,75,75,,,1640467527,1332668425,1380033115,1597665169,1639653,ERX4777846,ERS5435612,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.95086,0.95226,0.06292,0.0629,0.70341,0.70579,0.46524,0.46691,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10113,ERR4911022,ERX4777845,ERS5435611,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC MO rep2,SAMEA7678630,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678630|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep2|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC MO rep2 p,PGC MO rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 targeting MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_MO_PGC_rep2_R1.fastq.gz Tdrd7_MO_PGC_rep2_R2.fastq.gz,fastq fastq,906443913.0,6069224.0,E MTAB 9857:Tdrd7 MO PGC rep2 R,0:74.67 1:74.68,A:256935983;C:195137600;G:200975999;T:253026767;N:367564,74,74,,,256935983,195137600,200975999,253026767,367564,ERX4777845,ERS5435611,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93468,0.93603,0.09796,0.09848,0.7119,0.71439,0.48682,0.48933,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10114,ERR4911021,ERX4777844,ERS5435610,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC MO rep1,SAMEA7678629,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678629|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep1|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC MO rep1 p,PGC MO rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 targeting MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_MO_PGC_rep1_R1.fastq.gz Tdrd7_MO_PGC_rep1_R2.fastq.gz,fastq fastq,1078919524.0,7241200.0,E MTAB 9857:Tdrd7 MO PGC rep1 R,0:74.50 1:74.50,A:308200726;C:229836659;G:236649504;T:303673221;N:559414,74,74,,,308200726,229836659,236649504,303673221,559414,ERX4777844,ERS5435610,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.938,0.93748,0.10463,0.10431,0.7077,0.70999,0.48098,0.48239,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10115,ERR4911020,ERX4777843,ERS5435609,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 5mm rep2,SAMEA7678628,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678628|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep2|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC 5mm rep2 p,PGC 5mm rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 5mismatch MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_5mm_PGC_rep2_R1.fastq.gz Tdrd7_5mm_PGC_rep2_R2.fastq.gz,fastq fastq,673911944.0,4501723.0,E MTAB 9857:Tdrd7 5mm PGC rep2 R,0:74.85 1:74.85,A:184466911;C:150779527;G:155693395;T:182720480;N:251631,74,74,,,184466911,150779527,155693395,182720480,251631,ERX4777843,ERS5435609,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.91989,0.92025,0.08795,0.08919,0.70096,0.70416,0.49184,0.49415,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10116,ERR4911019,ERX4777842,ERS5435608,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 5mm rep1,SAMEA7678627,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678627|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep1|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC 5mm rep1 p,PGC 5mm rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 5mismatch MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_5mm_PGC_rep1_R1.fastq.gz Tdrd7_5mm_PGC_rep1_R2.fastq.gz,fastq fastq,565636692.0,3782000.0,E MTAB 9857:Tdrd7 5mm PGC rep1 R,0:74.78 1:74.78,A:157353454;C:124504476;G:128260137;T:155314004;N:204621,74,74,,,157353454,124504476,128260137,155314004,204621,ERX4777842,ERS5435608,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.91957,0.91995,0.08301,0.0845,0.69929,0.70195,0.48544,0.4877,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
39629,SRR1947863,SRX981062,SRS889614,SRP056748,PRJNA279991,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,PRJNA279991,Other,Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1  a bHLH transcription factor  has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species  and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa  the zebrafish homolog of mammalian Mesp1  lead to randomization of cardiac looping  together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly  the defect in asymmetry was found to occur independently of defects in the transient organ of laterality  the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling  and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects  and consistent with Mespaa over expression in this system  the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.,,,,Danio rerio injected with mespaa morpholino  5.5hpf,Zebrafish injected with mespaa morpholino,,strain:Ekkwill|dev stage:5.5hpf|sex:pooled male and female|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,Zebrafish injected with mespaa morpholino replicate 2,Zebrafish injected with mespaa morpholino replicate 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP056748,,loader:latf load,Mespa-230413_TGTGAA_L008_R2.fastq.gz Mespa-230413_TGTGAA_L008_R1.fastq.gz,fastq fastq,7275994449.0,42132158.0,RNAseq Danio rerio  5.5hpf  mespaa morpholino replicate2,0:101 1:101,A:2058072859;C:1476303521;G:1525105443;T:2088915957;N:127596669,101,101,,,2058072859,1476303521,1525105443,2088915957,127596669,SRX981062,SRS889614,SRA249481,Gladstone Institute|Bioinformatics,Gladstone Institutes,2,0.86631,0.83649,0.14484,0.22396,0.78861,0.90727,0.65055,0.64516,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2015-04-07,Gastrula,Embryo,Whole Organism,All anatomical structures
39630,SRR1947880,SRX981061,SRS895863,SRP056748,PRJNA279991,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,PRJNA279991,Other,Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1  a bHLH transcription factor  has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species  and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa  the zebrafish homolog of mammalian Mesp1  lead to randomization of cardiac looping  together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly  the defect in asymmetry was found to occur independently of defects in the transient organ of laterality  the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling  and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects  and consistent with Mespaa over expression in this system  the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.,,,,Danio rerio injected with negative control morpholino  5.5hpf,Zebrafish injected with untargeted negative control morpholino,,strain:Ekkwill|dev stage:5.5 hpf|sex:pooled male and female|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,Zebrafish injected with untargeted negative control morpholino replicate 2,Zebrafish injected with untargeted negative control morpholino replicate 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP056748,,loader:latf load,Std-230413_GTGTTA_L008_R1.fastq.gz Std-230413_GTGTTA_L008_R2.fastq.gz,fastq fastq,10015452496.0,49581448.0,RNAseq Danio rerio  5.5hpf  negative control morpholino replicate2,0:101 1:101,A:2883382922;C:1998043392;G:2046542450;T:2937071125;N:150412607,101,101,,,2883382922,1998043392,2046542450,2937071125,150412607,SRX981061,SRS895863,SRA249481,Gladstone Institute|Bioinformatics,Gladstone Institutes,2,0.8766,0.85002,0.17158,0.25762,0.77167,0.89057,0.64584,0.66342,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-03-31,Gastrula,Embryo,Whole Organism,All anatomical structures
39631,SRR1947876,SRX981011,SRS895863,SRP056748,PRJNA279991,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,PRJNA279991,Other,Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1  a bHLH transcription factor  has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species  and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa  the zebrafish homolog of mammalian Mesp1  lead to randomization of cardiac looping  together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly  the defect in asymmetry was found to occur independently of defects in the transient organ of laterality  the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling  and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects  and consistent with Mespaa over expression in this system  the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.,,,,Danio rerio injected with negative control morpholino  5.5hpf,Zebrafish injected with untargeted negative control morpholino,,strain:Ekkwill|dev stage:5.5 hpf|sex:pooled male and female|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,Zebrafish injected with untargeted negative control morpholino,Zebrafish injected with untargeted negative control morpholino replicate 1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP056748,,loader:latf load,Std-190413_ACACGA_L008_R2.fastq.gz Std-190413_ACACGA_L008_R1.fastq.gz,fastq fastq,10412449358.0,51546779.0,RNAseq Danio rerio  5.5hpf  negative control morpholino replicate1,0:101 1:101,A:2998996009;C:2064995108;G:2125498634;T:3066600855;N:156358752,101,101,,,2998996009,2064995108,2125498634,3066600855,156358752,SRX981011,SRS895863,SRA249481,Gladstone Institute|Bioinformatics,Gladstone Institutes,2,0.87394,0.84802,0.15672,0.23447,0.77072,0.89049,0.63241,0.65533,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-03-31,Gastrula,Embryo,Whole Organism,All anatomical structures
39632,SRR1947862,SRX974390,SRS889614,SRP056748,PRJNA279991,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,PRJNA279991,Other,Transcriptional events during initial vertebrate heart development in vivo remain poorly understood. Mesp1  a bHLH transcription factor  has been described as the earliest transcriptional regulator of cardiac progenitors in multiple species  and represents an excellent candidate for the investigation of relevant targets during cardiovascular development. We report here that both depletion and mutation of Mespaa  the zebrafish homolog of mammalian Mesp1  lead to randomization of cardiac looping  together with significant cardiac morphogenesis defects. These disruptions are preceded by a defect in cardiac left right asymmetry. Surprisingly  the defect in asymmetry was found to occur independently of defects in the transient organ of laterality  the Kupffer’s vesicle KV. We show that Mespaa regulates miR 430 expression during gastrulation to control the levels of Nodal signaling  and that this regulation is required for asymmetric laterality signaling in the prospective heart field. Ectopic expression of miR 430 is sufficient to induce cardiac laterality defects  and consistent with Mespaa over expression in this system  the reduction of miR 430 leads to cardia bifida. This study reveals a novel transcriptional regulation of miR 430 by Mespaa and a role for this pathway in cardiac laterality during gastrulation.,,,,Danio rerio injected with mespaa morpholino  5.5hpf,Zebrafish injected with mespaa morpholino,,strain:Ekkwill|dev stage:5.5hpf|sex:pooled male and female|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Mespaa regulates miR 430 expression during gastrulation and  initiates cardiac laterality,RNAseq analysis of mespaa knockdown embryos,Zebrafish injected with mespaa morpholino replicate 1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP056748,,loader:latf load,Mespa-190413_CACACA_L008_R2.fastq.gz Mespa-190413_CACACA_L008_R1.fastq.gz,fastq fastq,715965164.0,3668538.0,RNAseq Danio rerio  5.5hpf  mespaa morpholino replicate1,0:101 1:101,A:203464307;C:144071219;G:148845038;T:209200873;N:10383727,101,101,,,203464307,144071219,148845038,209200873,10383727,SRX974390,SRS889614,SRA249481,Gladstone Institute|Bioinformatics,Gladstone Institutes,2,0.86222,0.8307,0.14165,0.17545,0.7624,0.84415,0.65454,0.64758,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2015-04-07,Gastrula,Embryo,Whole Organism,All anatomical structures
41309,SRR4242454,SRX2163334,SRS1691357,SRP089876,PRJNA341782,Danio rerio Phenotype or Genotype,PRJNA341782,Other,Based on the differential comparison of transcriptomes of Homo   hetero zygote Het and wild type Wt  in vivo protein trap mutagenesis system  we have produced series of expression codex of the zebrafish. Here   we reported the transcriptomic characteristic of a line with stable deficits found in homozygous Homo expressing the strongest signal of red fluorescent protein mRFP in the central neural system and vascular system.,,,,,ho 160,,strain:TU|isolate:homozygous|age:3 dpf|dev stage:3 dpf|sex:not determined|tissue:whole fish|biomaterial provider:Intitute of Medical Sciences  University of Toronto  Toronto  Canada. Xiao yan WEN|birth date:2015 05 01|genotype:homozygous|phenotype:small head  abnormal vascular system|treatment:in vivo protein trap mutagenesis|BioSampleModel:Model organism or animal,,,,,,,,,1,ho 160,ho 160,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP089876,,,HO.fq.gz,fastq,568688414.0,11605886.0,HO.fq.gz,0:49,A:146833011;C:136838940;G:142141532;T:142831489;N:43442,49,,,,146833011,136838940,142141532,142831489,43442,SRX2163334,SRS1691357,SRA471230,Guangdong Ocean University|Fisheries College,Guangdong Ocean University,1,0.92072,,0.03662,,0.79584,,0.46051,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-09-14,Larval,Larval,Whole Organism,All anatomical structures
41310,SRR4242453,SRX2163333,SRS1691356,SRP089876,PRJNA341782,Danio rerio Phenotype or Genotype,PRJNA341782,Other,Based on the differential comparison of transcriptomes of Homo   hetero zygote Het and wild type Wt  in vivo protein trap mutagenesis system  we have produced series of expression codex of the zebrafish. Here   we reported the transcriptomic characteristic of a line with stable deficits found in homozygous Homo expressing the strongest signal of red fluorescent protein mRFP in the central neural system and vascular system.,,,,,he 160,,strain:TU|isolate:heterozygous|age:3 dpf|dev stage:3 dpf|sex:not determined|tissue:whole fish|biomaterial provider:Intitute of Medical Sciences  University of Toronto  Toronto  Canada. Xiao yan WEN|birth date:2015 05 01|genotype:heterozygous|phenotype:normal|treatment:in vivo protein trap mutagenesis|BioSampleModel:Model organism or animal,,,,,,,,,1,he 160,he 160,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP089876,,,HE.fq,fastq,578835432.0,11812968.0,HE.fq,0:49,A:149797321;C:137638814;G:143656076;T:147699087;N:44134,49,,,,149797321,137638814,143656076,147699087,44134,SRX2163333,SRS1691356,SRA471230,Guangdong Ocean University|Fisheries College,Guangdong Ocean University,1,0.96392,,0.03868,,0.71064,,0.48997,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-09-19,Larval,Larval,Whole Organism,All anatomical structures
41311,SRR4242452,SRX2163332,SRS1691355,SRP089876,PRJNA341782,Danio rerio Phenotype or Genotype,PRJNA341782,Other,Based on the differential comparison of transcriptomes of Homo   hetero zygote Het and wild type Wt  in vivo protein trap mutagenesis system  we have produced series of expression codex of the zebrafish. Here   we reported the transcriptomic characteristic of a line with stable deficits found in homozygous Homo expressing the strongest signal of red fluorescent protein mRFP in the central neural system and vascular system.,,,,,wt 160,,strain:TU|isolate:wild type|age:3 dpf|dev stage:3 dpf|sex:not determined|tissue:whole fish|biomaterial provider:Intitute of Medical Sciences  University of Toronto  Toronto  Canada. Xiao yan WEN|birth date:2015 05 01|genotype:wild type|phenotype:normal|BioSampleModel:Model organism or animal,,,,,,,,,1,wt 160,wt 160,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP089876,,,WT.fq.gz,fastq,582208151.0,11881799.0,WT.fq.gz,0:49,A:151848733;C:138129346;G:143758419;T:148430704;N:40949,49,,,,151848733,138129346,143758419,148430704,40949,SRX2163332,SRS1691355,SRA471230,Guangdong Ocean University|Fisheries College,Guangdong Ocean University,1,0.95342,,0.04301,,0.75503,,0.48726,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-09-19,Larval,Larval,Whole Organism,All anatomical structures
41349,SRR4330940,SRX2205508,SRS1723862,SRP090717,PRJNA345071,Transcriptome sequencing of zebrafish mutants,PRJNA345071,Other,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf  and used for transcriptome sequencing.,,,,,ZIS 3,,strain:mutant biological replicate 3|dev stage:10 dpf|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2015 08|breeding method:?artificial insemination|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish mutant at 10 dpf,ZIS 3,ZIS 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP090717,,,ZIS-3_S41_L003_R1_001.fastq ZIS-3_S41_L003_R2_001.fastq,fastq fastq,8951074036.0,29639318.0,ZIS 3 S41 L003 R1 001.fastq,0:151 1:151,A:2283207699;C:2181203331;G:2250920956;T:2233298555;N:2443495,151,151,,,2283207699,2181203331,2250920956,2233298555,2443495,SRX2205508,SRS1723862,SRA481515,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94568,0.94599,0.04792,0.04705,0.68511,0.69191,0.48349,0.49441,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-31,Larval,Larval,Whole Organism,All anatomical structures
41350,SRR4330939,SRX2205507,SRS1723861,SRP090717,PRJNA345071,Transcriptome sequencing of zebrafish mutants,PRJNA345071,Other,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf  and used for transcriptome sequencing.,,,,,ZIS 2,,strain:mutant biological replicate 2|dev stage:10 dpf|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2015 08|breeding method:?artificial insemination|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish mutant at 10 dpf,ZIS 2,ZIS 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP090717,,,ZIS-2_S40_L003_R1_001.fastq ZIS-2_S40_L003_R2_001.fastq,fastq fastq,9435991208.0,31245004.0,ZIS 2 S40 L003 R2 001.fastq,0:151 1:151,A:2432777029;C:2274473737;G:2351228268;T:2374883671;N:2628503,151,151,,,2432777029,2274473737,2351228268,2374883671,2628503,SRX2205507,SRS1723861,SRA481515,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93852,0.93895,0.06814,0.06752,0.67464,0.68185,0.4731,0.48737,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-31,Larval,Larval,Whole Organism,All anatomical structures
41351,SRR4330938,SRX2205506,SRS1723859,SRP090717,PRJNA345071,Transcriptome sequencing of zebrafish mutants,PRJNA345071,Other,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf  and used for transcriptome sequencing.,,,,,ZIS 1,,strain:mutant biological replicate 1|dev stage:10 dpf|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2015 08|breeding method:?artificial insemination|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish mutant at 10 dpf,ZIS 1,ZIS 1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP090717,,,ZIS-1_S58_L004_R1_001.fastq ZIS-1_S58_L004_R2_001.fastq,fastq fastq,9474125956.0,31371278.0,ZIS 1 S58 L004 R1 001.fastq,0:151 1:151,A:2432127105;C:2294541938;G:2369906198;T:2374445988;N:3104727,151,151,,,2432127105,2294541938,2369906198,2374445988,3104727,SRX2205506,SRS1723859,SRA481515,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94217,0.94136,0.05812,0.05769,0.67957,0.68665,0.48986,0.48912,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-31,Larval,Larval,Whole Organism,All anatomical structures
41352,SRR4330937,SRX2205505,SRS1723863,SRP090717,PRJNA345071,Transcriptome sequencing of zebrafish mutants,PRJNA345071,Other,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf  and used for transcriptome sequencing.,,,,,WT 3,,strain:wild type biological replicate 3|dev stage:10 dpf|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2015 08|breeding method:?artificial insemination|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 10 dpf,WT 3,WT 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP090717,,,WT-3_S59_L004_R1_001.fastq WT-3_S59_L004_R2_001.fastq,fastq fastq,9459728710.0,31323605.0,WT 3 S59 L004 R2 001.fastq,0:151 1:151,A:2435834973;C:2283457751;G:2353515662;T:2383834638;N:3085686,151,151,,,2435834973,2283457751,2353515662,2383834638,3085686,SRX2205505,SRS1723863,SRA481515,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93703,0.93671,0.06932,0.06902,0.67815,0.68527,0.49406,0.48629,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-31,Larval,Larval,Whole Organism,All anatomical structures
41353,SRR4330936,SRX2205504,SRS1723860,SRP090717,PRJNA345071,Transcriptome sequencing of zebrafish mutants,PRJNA345071,Other,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf  and used for transcriptome sequencing.,,,,,WT 2,,strain:wild type biological replicate 2|dev stage:10 dpf|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2015 08|breeding method:?artificial insemination|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 10 dpf,WT 2,WT 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP090717,,,WT-2_S39_L003_R1_001.fastq WT-2_S39_L003_R2_001.fastq,fastq fastq,8115257628.0,26871714.0,WT 2 S39 L003 R1 001.fastq,0:151 1:151,A:2056302105;C:1991691115;G:2061808328;T:2003236611;N:2219469,151,151,,,2056302105,1991691115,2061808328,2003236611,2219469,SRX2205504,SRS1723860,SRA481515,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.9479,0.94848,0.03505,0.0349,0.69946,0.70638,0.4871,0.48737,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-31,Larval,Larval,Whole Organism,All anatomical structures
41354,SRR4330935,SRX2205503,SRS1723858,SRP090717,PRJNA345071,Transcriptome sequencing of zebrafish mutants,PRJNA345071,Other,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf  and used for transcriptome sequencing.,,,,,WT 1,,strain:wild type biological replicate 1|dev stage:10 dpf|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2015 08|breeding method:?artificial insemination|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 10 dpf,WT 1,WT 1,To investigate the possible mechanism that NOD1 impacts larval survival in zebrafish  we performed transcriptome analysis to explore NOD1 related signaling pathways. Zebrafish larvae from WT and NOD1 1IS /  were collected at 10 dpf and used for transcriptome sequencing.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP090717,,,WT-1_S38_L003_R1_001.fastq WT-1_S38_L003_R2_001.fastq,fastq fastq,9771991274.0,32357587.0,WT 1 S38 L003 R2 001.fastq,0:151 1:151,A:2524417259;C:2348903783;G:2421563752;T:2474419170;N:2687310,151,151,,,2524417259,2348903783,2421563752,2474419170,2687310,SRX2205503,SRS1723858,SRA481515,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93787,0.93896,0.0697,0.06907,0.67446,0.68162,0.49385,0.49554,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-31,Larval,Larval,Whole Organism,All anatomical structures
41603,SRR5086607,SRX2403900,SRS1843204,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,RIP2 Etarda 2,,isolate:RIP2 mutant biological replicate 2|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RIP2 mutant at 7 dpf,RIP2 Etarda 2,RIP2 Etarda 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-RP-E-tarda-2_L003_R2.fastq.gz S231_07B_CHG009012-0413lane6-RP-E-tarda-2_L003_R1.fastq.gz,fastq fastq,12903564000.0,43011880.0,S231 07B CHG009012 0413lane6 RP E tarda 2 L003 R1.fastq.gz,0:150 1:150,A:3540121379;C:2905716861;G:3027503729;T:3429809429;N:412602,150,150,,,3540121379,2905716861,3027503729,3429809429,412602,SRX2403900,SRS1843204,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.91895,0.92448,0.22816,0.22865,0.6873,0.69104,0.59821,0.59683,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-12-08,Larval,Larval,Whole Organism,All anatomical structures
41604,SRR5086606,SRX2403899,SRS1843203,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,NOD1 Etarda 1,,isolate:NOD1 mutant biological replicate 1|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish NOD1 mutant at 7 dpf,NOD1 Etarda 1,NOD1 Etarda 1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-ND-E-tarda-1_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-ND-E-tarda-1_L003_R2.fastq.gz,fastq fastq,12320572500.0,41068575.0,S231 07B CHG009012 0413lane6 ND E tarda 1 L003 R1.fastq.gz,0:150 1:150,A:3355646078;C:2797387103;G:2920550779;T:3246590603;N:397937,150,150,,,3355646078,2797387103,2920550779,3246590603,397937,SRX2403899,SRS1843203,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.86604,0.87043,0.20071,0.20146,0.69369,0.69869,0.5907,0.59843,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41605,SRR5086605,SRX2403898,SRS1843202,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,NOD1 Etarda 2,,isolate:NOD1 mutant biological replicate 2|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish NOD1 mutant at 7 dpf,NOD1 Etarda 2,NOD1 Etarda 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-ND-E-tarda-2_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-ND-E-tarda-2_L003_R2.fastq.gz,fastq fastq,15551299800.0,51837666.0,S231 07B CHG009012 0413lane6 ND E tarda 2 L003 R1.fastq.gz,0:150 1:150,A:4265070757;C:3495006741;G:3648563581;T:4142124454;N:534267,150,150,,,4265070757,3495006741,3648563581,4142124454,534267,SRX2403898,SRS1843202,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.86759,0.86834,0.23528,0.23586,0.68779,0.69272,0.57804,0.57769,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41606,SRR5086604,SRX2403897,SRS1843201,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,RIP2 Etarda 3,,isolate:RIP2 mutant biological replicate 3|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RIP2 mutant at 7 dpf,RIP2 Etarda 3,RIP2 Etarda 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-RP-E-tarda-3_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-RP-E-tarda-3_L003_R2.fastq.gz,fastq fastq,12144058200.0,40480194.0,S231 07B CHG009012 0413lane6 RP E tarda 3 L003 R1.fastq.gz,0:150 1:150,A:3277198817;C:2779538400;G:2897367228;T:3189540397;N:413358,150,150,,,3277198817,2779538400,2897367228,3189540397,413358,SRX2403897,SRS1843201,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.91654,0.9175,0.25593,0.25637,0.68795,0.69414,0.56468,0.56806,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41607,SRR5086603,SRX2403896,SRS1843200,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,WT Etarda 3,,isolate:wild type biological replicate 3|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 7 dpf,WT Etarda 3,WT Etarda 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-WT-E-tarda-3_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-WT-E-tarda-3_L003_R2.fastq.gz,fastq fastq,13158784200.0,43862614.0,S231 07B CHG009012 0413lane6 WT E tarda 3 L003 R1.fastq.gz,0:150 1:150,A:3492740553;C:3076792456;G:3216533074;T:3372287751;N:430366,150,150,,,3492740553,3076792456,3216533074,3372287751,430366,SRX2403896,SRS1843200,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.91602,0.92416,0.23246,0.23514,0.68164,0.68663,0.55407,0.55215,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41608,SRR5086602,SRX2403895,SRS1843199,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,WT Etarda 1,,isolate:wild type biological replicate 1|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 7dpf,WT Etarda 1,WT Etarda 1,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-WT-E-tarda-1_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-WT-E-tarda-1_L003_R2.fastq.gz,fastq fastq,11991766500.0,39972555.0,S231 07B CHG009012 0413lane6 WT E tarda 1 L003 R1.fastq.gz,0:150 1:150,A:3282107515;C:2699757677;G:2810716102;T:3198780035;N:405171,150,150,,,3282107515,2699757677,2810716102,3198780035,405171,SRX2403895,SRS1843199,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.91731,0.91778,0.23094,0.23042,0.6784,0.68596,0.59413,0.59241,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41609,SRR5086601,SRX2403894,SRS1843198,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,NOD1 Etarda 3,,isolate:NOD1 mutant biological replicate 3|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish NOD1 mutant at 7 dpf,NOD1 Etarda 3,NOD1 Etarda 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-ND-E-tarda-3_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-ND-E-tarda-3_L003_R2.fastq.gz,fastq fastq,13231011300.0,44103371.0,S231 07B CHG009012 0413lane6 ND E tarda 3 L003 R1.fastq.gz,0:150 1:150,A:3583948856;C:3022120866;G:3144073054;T:3480438095;N:430429,150,150,,,3583948856,3022120866,3144073054,3480438095,430429,SRX2403894,SRS1843198,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.8625,0.86327,0.21095,0.21123,0.69126,0.69808,0.59807,0.59873,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41610,SRR5086600,SRX2403893,SRS1843197,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,WT Etarda 2,,isolate:wild type biological replicate 2|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 7 dpf,WT Etarda 2,WT Etarda 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-WT-E-tarda-2_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-WT-E-tarda-2_L003_R2.fastq.gz,fastq fastq,11385997200.0,37953324.0,S231 07B CHG009012 0413lane6 WT E tarda 2 L003 R1.fastq.gz,0:150 1:150,A:3100666193;C:2581361422;G:2676308702;T:3027299840;N:361043,150,150,,,3100666193,2581361422,2676308702,3027299840,361043,SRX2403893,SRS1843197,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.91592,0.91843,0.23215,0.23276,0.67894,0.6843,0.56756,0.57405,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41611,SRR5086599,SRX2403892,SRS1843196,SRP094738,PRJNA356682,Transcriptome sequencing of zebrafish mutants with or without xxx tarda infection,PRJNA356682,Other,To investigate the possible mechanism that NOD1/RIP2 impacts larval survival in zebrafish under infectious condition  we performed transcriptome analysis. Zebrafish larvae from WT  NOD1 /  and RIP /  were infected with Edwardsiella tarda  and collected at 24 hours post infection hpi.,,,,,RIP2 Etarda 1,,isolate:RIP2 mutant biological replicate 1|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RIP2 mutant at 7 dpf,RIP2 Etarda 1,RIP2 Etarda 1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP094738,,,S231_07B_CHG009012-0413lane6-RP-E-tarda-1_L003_R1.fastq.gz S231_07B_CHG009012-0413lane6-RP-E-tarda-1_L003_R2.fastq.gz,fastq fastq,12517987200.0,41726624.0,S231 07B CHG009012 0413lane6 RP E tarda 1 L003 R1.fastq.gz,0:150 1:150,A:3383702176;C:2864897363;G:2969958296;T:3299042555;N:386810,150,150,,,3383702176,2864897363,2969958296,3299042555,386810,SRX2403892,SRS1843196,SRA501516,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.92847,0.93046,0.20764,0.20908,0.68217,0.68889,0.58846,0.59063,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-11-27,Larval,Larval,Whole Organism,All anatomical structures
41754,SRR5131065,SRX2444929,SRS1878801,SRP095651,PRJNA358793,Transcriptome sequencing of zebrafish RIP2 mutants,PRJNA358793,Other,Zebrafish larvae from wildtype and RIP2 /  were collected at 7 dpf  and used for transcriptome sequencing.,,,,,control 3,,isolate:wild type biological replicate 3|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 7 dpf,control 3,control 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP095651,,,S231_07B_CHG009010-0413lane4-WT-3_L001_R2.fastq.gz S231_07B_CHG009010-0413lane4-WT-3_L001_R1.fastq.gz,fastq fastq,7170870300.0,23902901.0,S231 07B CHG009010 0413lane4 WT 3 L001 R2.fastq.gz,0:150 1:150,A:1861223343;C:1713993670;G:1720465419;T:1875067010;N:120858,150,150,,,1861223343,1713993670,1720465419,1875067010,120858,SRX2444929,SRS1878801,SRA510115,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93719,0.93331,0.07804,0.07734,0.66478,0.67152,0.48991,0.48846,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2016-12-25,Larval,Larval,Whole Organism,All anatomical structures
41755,SRR5131064,SRX2444928,SRS1878800,SRP095651,PRJNA358793,Transcriptome sequencing of zebrafish RIP2 mutants,PRJNA358793,Other,Zebrafish larvae from wildtype and RIP2 /  were collected at 7 dpf  and used for transcriptome sequencing.,,,,,RP 3,,isolate:RIP2 mutant biological replicate 3|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RIP2 mutant at 7 dpf,RP 3,RP 3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP095651,,,S231_07B_CHG009010-0413lane4-RP-3_L001_R1.fastq.gz S231_07B_CHG009010-0413lane4-RP-3_L001_R2.fastq.gz,fastq fastq,7468205400.0,24894018.0,S231 07B CHG009010 0413lane4 RP 3 L001 R1.fastq.gz,0:150 1:150,A:1923116988;C:1800729614;G:1804880487;T:1939349442;N:128869,150,150,,,1923116988,1800729614,1804880487,1939349442,128869,SRX2444928,SRS1878800,SRA510115,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94182,0.93791,0.07003,0.06911,0.67391,0.68032,0.48725,0.48383,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-12-21,Larval,Larval,Whole Organism,All anatomical structures
41756,SRR5131063,SRX2444927,SRS1878799,SRP095651,PRJNA358793,Transcriptome sequencing of zebrafish RIP2 mutants,PRJNA358793,Other,Zebrafish larvae from wildtype and RIP2 /  were collected at 7 dpf  and used for transcriptome sequencing.,,,,,control 1,,isolate:wild type biological replicate 1|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 7dpf,control 1,control 1,To investigate the possible mechanism that RIP2 impacts immune response in zebrafish  we performed transcriptome analysis. Zebrafish larvae from WT and RIP /  were collected at 7 dpf.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP095651,,,S231_07B_CHG009010-0413lane4-WT-1_L001_R1.fastq.gz S231_07B_CHG009010-0413lane4-WT-1_L001_R2.fastq.gz,fastq fastq,7794774600.0,25982582.0,S231 07B CHG009010 0413lane4 WT 1 L001 R1.fastq.gz,0:150 1:150,A:2030478380;C:1854310335;G:1862519444;T:2047324790;N:141651,150,150,,,2030478380,1854310335,1862519444,2047324790,141651,SRX2444927,SRS1878799,SRA510115,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94149,0.93653,0.07296,0.07218,0.66614,0.67294,0.49615,0.48813,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-12-21,Larval,Larval,Whole Organism,All anatomical structures
41757,SRR5131062,SRX2444926,SRS1878798,SRP095651,PRJNA358793,Transcriptome sequencing of zebrafish RIP2 mutants,PRJNA358793,Other,Zebrafish larvae from wildtype and RIP2 /  were collected at 7 dpf  and used for transcriptome sequencing.,,,,,control 2,,isolate:wild type biological replicate 2|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish wildtype at 7 dpf,control 2,control 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP095651,,,S231_07B_CHG009010-0413lane4-WT-2_L001_R1.fastq.gz S231_07B_CHG009010-0413lane4-WT-2_L001_R2.fastq.gz,fastq fastq,5623326600.0,18744422.0,S231 07B CHG009010 0413lane4 WT 2 L001 R2.fastq.gz,0:150 1:150,A:1451164902;C:1350358314;G:1359170147;T:1462531546;N:101691,150,150,,,1451164902,1350358314,1359170147,1462531546,101691,SRX2444926,SRS1878798,SRA510115,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93864,0.93904,0.06797,0.06755,0.67048,0.67521,0.49371,0.48819,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-12-21,Larval,Larval,Whole Organism,All anatomical structures
41758,SRR5131061,SRX2444925,SRS1878797,SRP095651,PRJNA358793,Transcriptome sequencing of zebrafish RIP2 mutants,PRJNA358793,Other,Zebrafish larvae from wildtype and RIP2 /  were collected at 7 dpf  and used for transcriptome sequencing.,,,,,RP 1,,isolate:RIP2 mutant biological replicate 1|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RIP2 mutant at 7 dpf,RP 1,RP 1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP095651,,,S231_07B_CHG009010-0413lane4-RP-1_L001_R1.fastq.gz S231_07B_CHG009010-0413lane4-RP-1_L001_R2.fastq.gz,fastq fastq,8583762600.0,28612542.0,S231 07B CHG009010 0413lane4 RP 1 L001 R2.fastq.gz,0:150 1:150,A:2233488442;C:2047436003;G:2053585249;T:2249097620;N:155286,150,150,,,2233488442,2047436003,2053585249,2249097620,155286,SRX2444925,SRS1878797,SRA510115,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94045,0.93559,0.08356,0.0825,0.66576,0.67188,0.48456,0.48745,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-12-21,Larval,Larval,Whole Organism,All anatomical structures
41759,SRR5131060,SRX2444924,SRS1878796,SRP095651,PRJNA358793,Transcriptome sequencing of zebrafish RIP2 mutants,PRJNA358793,Other,Zebrafish larvae from wildtype and RIP2 /  were collected at 7 dpf  and used for transcriptome sequencing.,,,,,RP 2,,isolate:RIP2 mutant biological replicate 2|age:7 dpf|dev stage:larvae|sex:pooled male and female|tissue:larvae|biomaterial provider:Chang MX|birth date:2016 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish RIP2 mutant at 7 dpf,RP 2,RP 2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP095651,,,S231_07B_CHG009010-0413lane4-RP-2_L001_R1.fastq.gz S231_07B_CHG009010-0413lane4-RP-2_L001_R2.fastq.gz,fastq fastq,6660884700.0,22202949.0,S231 07B CHG009010 0413lane4 RP 2 L001 R1.fastq.gz,0:150 1:150,A:1716524391;C:1604826566;G:1610050455;T:1729364340;N:118948,150,150,,,1716524391,1604826566,1610050455,1729364340,118948,SRX2444924,SRS1878796,SRA510115,"Institute of Hydrobiology, Chinese Academy of Sciences|Center for Fish Biology and Fishery Biotechnology","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.94509,0.94069,0.07191,0.0702,0.67322,0.68045,0.4937,0.4864,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-12-21,Larval,Larval,Whole Organism,All anatomical structures
55655,SRR10674410,SRX7351703,SRS5811186,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 100 1,,isolate:biologocal replicate 10|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050110,bps050110,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_100_1_1.fq.gz BPS_100_1_2.fq.gz,fastq fastq,6958801200.0,69588012.0,BPS 100 1 1.fq.gz,0:100 1:100,A:1852139865;C:1635606671;G:1596180575;T:1874072794;N:801295,100,100,,,1852139865,1635606671,1596180575,1874072794,801295,SRX7351703,SRS5811186,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94716,,0.09824,,0.68475,,0.47195,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55656,SRR10674411,SRX7351702,SRS5811185,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 10 3,,isolate:biologocal replicate 9|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050109,bps050109,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_10_3_1.fq.gz BPS_10_3_2.fq.gz,fastq fastq,6969574800.0,69695748.0,BPS 10 3 1.fq.gz,0:100 1:100,A:1860393053;C:1631995190;G:1597357772;T:1879188120;N:640665,100,100,,,1860393053,1631995190,1597357772,1879188120,640665,SRX7351702,SRS5811185,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94597,,0.10542,,0.68016,,0.4666,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55657,SRR10674412,SRX7351701,SRS5811182,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 10 2,,isolate:biologocal replicate 8|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050108,bps050108,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_10_2_1.fq.gz BPS_10_2_2.fq.gz,fastq fastq,6709340400.0,67093404.0,BPS 10 2 1.fq.gz,0:100 1:100,A:2036224090;C:1319652145;G:1297564214;T:2055258677;N:641274,100,100,,,2036224090,1319652145,1297564214,2055258677,641274,SRX7351701,SRS5811182,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.87778,,0.38111,,0.71543,,0.56061,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55658,SRR10674413,SRX7351700,SRS5811181,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 10 1,,isolate:biologocal replicate 7|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050107,bps050107,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_10_1_1.fq.gz BPS_10_1_2.fq.gz,fastq fastq,6717746800.0,67177468.0,BPS 10 1 1.fq.gz,0:100 1:100,A:1787637885;C:1578942212;G:1548400030;T:1802147201;N:619472,100,100,,,1787637885,1578942212,1548400030,1802147201,619472,SRX7351700,SRS5811181,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94726,,0.10123,,0.68919,,0.45234,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55659,SRR10674414,SRX7351699,SRS5811184,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 1 3,,isolate:biologocal replicate 6|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050106,bps050106,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_1_3_2.fq.gz BPS_1_3_1.fq.gz,fastq fastq,6726522800.0,67265228.0,BPS 1 3 1.fq.gz,0:100 1:100,A:1789486049;C:1582069064;G:1548432478;T:1805913744;N:621465,100,100,,,1789486049,1582069064,1548432478,1805913744,621465,SRX7351699,SRS5811184,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.9465,,0.09858,,0.68442,,0.45032,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55660,SRR10674415,SRX7351698,SRS5811180,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 1 2,,isolate:biologocal replicate 5|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050105,bps050105,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_1_2_2.fq.gz BPS_1_2_1.fq.gz,fastq fastq,6959685000.0,69596850.0,BPS 1 2 1.fq.gz,0:100 1:100,A:1914426129;C:1574998719;G:1542052351;T:1927550147;N:657654,100,100,,,1914426129,1574998719,1542052351,1927550147,657654,SRX7351698,SRS5811180,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94034,,0.14574,,0.69934,,0.47033,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55661,SRR10674416,SRX7351697,SRS5811183,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 1 1,,isolate:biologocal replicate 4|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050104,bps050104,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_1_1_1.fq.gz BPS_1_1_2.fq.gz,fastq fastq,7040826400.0,70408264.0,BPS 1 1 1.fq.gz,0:100 1:100,A:1915125100;C:1612334047;G:1578924466;T:1933922418;N:520369,100,100,,,1915125100,1612334047,1578924466,1933922418,520369,SRX7351697,SRS5811183,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94114,,0.13158,,0.68903,,0.47739,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55662,SRR10674417,SRX7351696,SRS5811179,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 0 1 3,,isolate:biologocal replicate 3|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050103,bps050103,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_0_1_3_1.fq.gz BPS_0_1_3_2.fq.gz,fastq fastq,6992676800.0,69926768.0,BPS 0 1 3 1.fq.gz,0:100 1:100,A:1860627581;C:1643489002;G:1610508221;T:1877536968;N:515028,100,100,,,1860627581,1643489002,1610508221,1877536968,515028,SRX7351696,SRS5811179,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94485,,0.101,,0.68314,,0.45711,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55663,SRR10674418,SRX7351695,SRS5811178,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,Cntrol3,,isolate:biologocal replicate 18|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050118,bps050118,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,Cntrol3_1.fq.gz Cntrol3_2.fq.gz,fastq fastq,6742983200.0,67429832.0,Cntrol3 1.fq.gz,0:100 1:100,A:1801392073;C:1577630219;G:1545614005;T:1817857809;N:489094,100,100,,,1801392073,1577630219,1545614005,1817857809,489094,SRX7351695,SRS5811178,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94386,,0.10779,,0.68832,,0.45545,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55664,SRR10674419,SRX7351694,SRS5811177,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,Cntrol2,,isolate:biologocal replicate 17|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050117,bps050117,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,Cntrol2_1.fq.gz Cntrol2_2.fq.gz,fastq fastq,6750661000.0,67506610.0,Cntrol2 1.fq.gz,0:100 1:100,A:1796606666;C:1585909518;G:1556014239;T:1811284557;N:846020,100,100,,,1796606666,1585909518,1556014239,1811284557,846020,SRX7351694,SRS5811177,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94397,,0.10007,,0.68708,,0.47779,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55665,SRR10674420,SRX7351693,SRS5811174,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,Cntrol1,,isolate:biologocal replicate 16|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050116,bps050116,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,Cntrol1_1.fq.gz Cntrol1_2.fq.gz,fastq fastq,6766663000.0,67666630.0,Cntrol1 1.fq.gz,0:100 1:100,A:1825736389;C:1564390057;G:1532835305;T:1842876742;N:824507,100,100,,,1825736389,1564390057,1532835305,1842876742,824507,SRX7351693,SRS5811174,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94047,,0.12338,,0.68893,,0.46407,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55666,SRR10674421,SRX7351692,SRS5811176,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 1000 3,,isolate:biologocal replicate 15|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050115,bps050115,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_1000_3_1.fq.gz BPS_1000_3_2.fq.gz,fastq fastq,6507622200.0,65076222.0,BPS 1000 3 1.fq.gz,0:100 1:100,A:1735402948;C:1525938362;G:1493787016;T:1751945676;N:548198,100,100,,,1735402948,1525938362,1493787016,1751945676,548198,SRX7351692,SRS5811176,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94304,,0.10593,,0.6842,,0.46348,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55667,SRR10674422,SRX7351691,SRS5811173,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 1000 2,,isolate:biologocal replicate 14|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050114,bps050114,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_1000_2_1.fq.gz BPS_1000_2_2.fq.gz,fastq fastq,6740712000.0,67407120.0,BPS 1000 2 1.fq.gz,0:100 1:100,A:1816870993;C:1562402111;G:1527381283;T:1833284067;N:773546,100,100,,,1816870993,1562402111,1527381283,1833284067,773546,SRX7351691,SRS5811173,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94327,,0.11511,,0.70033,,0.4551,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55668,SRR10674423,SRX7351690,SRS5811175,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 1000 1,,isolate:biologocal replicate 13|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050113,bps050113,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_1000_1_1.fq.gz BPS_1000_1_2.fq.gz,fastq fastq,6727750400.0,67277504.0,BPS 1000 1 1.fq.gz,0:100 1:100,A:1803578734;C:1568712705;G:1535618959;T:1819016739;N:823263,100,100,,,1803578734,1568712705,1535618959,1819016739,823263,SRX7351690,SRS5811175,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94457,,0.1118,,0.69087,,0.46815,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55669,SRR10674424,SRX7351689,SRS5811172,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 100 3,,isolate:biologocal replicate 12|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050112,bps050112,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_100_3_1.fq.gz BPS_100_3_2.fq.gz,fastq fastq,6962431800.0,69624318.0,BPS 100 3 1.fq.gz,0:100 1:100,A:1865300693;C:1624120289;G:1585691091;T:1886538935;N:780792,100,100,,,1865300693,1624120289,1585691091,1886538935,780792,SRX7351689,SRS5811172,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94581,,0.10195,,0.68288,,0.47174,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55670,SRR10674425,SRX7351688,SRS5811171,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 100 2,,isolate:biologocal replicate 11|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050111,bps050111,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_100_2_1.fq.gz BPS_100_2_2.fq.gz,fastq fastq,7201035800.0,72010358.0,BPS 100 2 1.fq.gz,0:100 1:100,A:2115590854;C:1489181336;G:1459936470;T:2135514629;N:812511,100,100,,,2115590854,1489181336,1459936470,2135514629,812511,SRX7351688,SRS5811171,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.90678,,0.29289,,0.70735,,0.49554,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55671,SRR10674426,SRX7351687,SRS5811170,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 0 1 2,,isolate:biologocal replicate 2|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050102,bps050102,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_0_1_2_1.fq.gz BPS_0_1_2_2.fq.gz,fastq fastq,7022382800.0,70223828.0,BPS 0 1 2 1.fq.gz,0:100 1:100,A:1853514579;C:1663935080;G:1635277415;T:1869136960;N:518766,100,100,,,1853514579,1663935080,1635277415,1869136960,518766,SRX7351687,SRS5811170,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94712,,0.09313,,0.6814,,0.47256,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
55672,SRR10674427,SRX7351686,SRS5811167,SRP237283,PRJNA595113,Transcriptomic responses of Bisphenol S on zebrafish,PRJNA595113,Other,To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure  global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure  we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.,,,,,BPS 0 1 1,,isolate:biologocal replicate 1|age:120hpf|sex:not collected|tissue:embryo|collection date:2018 05 01|geo loc name:China:Guangdong|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic responses of Bisphenol S,bps050101,bps050101,An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent  Santa Clara  CA  USA with only high quality RNA samples 28 S:18 S=2.02.2  RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen  China . The libraries were sequenced at the Beijing Genomics Institute BGI  Shenzhen  China on a BGISEQ500 platform with 50 bp single end reads  under three replicates per treatment group.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP237283,,,BPS_0_1_1_1.fq.gz BPS_0_1_1_2.fq.gz,fastq fastq,7013900400.0,70139004.0,BPS 0 1 1 1.fq.gz,0:100 1:100,A:1885826391;C:1629114228;G:1597181244;T:1901261511;N:517026,100,100,,,1885826391,1629114228,1597181244,1901261511,517026,SRX7351686,SRS5811167,SRA1010884,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.94226,,0.11616,,0.69014,,0.45679,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-12-12,Larval,Larval,Embryo Imprecise,All anatomical structures
60445,SRR12272862,SRX8777892,SRS7048444,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_2_4.fq,fastq,542610936.0,21965958.0,C2 C2 2 4.fq.gz,0:24.70,A:95221617;C:122628624;G:167025611;T:157730855;N:4229,24,,,,95221617,122628624,167025611,157730855,4229,SRX8777892,SRS7048444,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.8119,,0.10745,,0.85717,,0.51338,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60446,SRR12272863,SRX8777891,SRS7048443,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_1_4.fq,fastq,542847476.0,22614181.0,C2 C2 1 4.fq.gz,0:24.00,A:99999101;C:125407906;G:162383758;T:155055099;N:1612,24,,,,99999101,125407906,162383758,155055099,1612,SRX8777891,SRS7048443,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84327,,0.10491,,0.83256,,0.52046,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60447,SRR12272864,SRX8777890,SRS7048442,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_2_4.fq,fastq,570918284.0,22577002.0,C1 C1 2 4.fq.gz,0:25.29,A:100121235;C:130480588;G:178656113;T:161652765;N:7583,25,,,,100121235,130480588,178656113,161652765,7583,SRX8777890,SRS7048442,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.85096,,0.12542,,0.82873,,0.51535,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60448,SRR12272865,SRX8777889,SRS7048441,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_1_4.fq,fastq,545089417.0,22812164.0,C1 C1 1 4.fq.gz,0:23.89,A:99851844;C:125314095;G:166401335;T:153521167;N:976,23,,,,99851844,125314095,166401335,153521167,976,SRX8777889,SRS7048441,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84602,,0.11725,,0.83159,,0.51353,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60449,SRR12272866,SRX8777888,SRS7048440,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_2_4.fq,fastq,527443144.0,23174740.0,C0 C0 2 4.fq.gz,0:22.76,A:102368401;C:120843229;G:151690193;T:152540806;N:515,22,,,,102368401,120843229,151690193,152540806,515,SRX8777888,SRS7048440,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83063,,0.08114,,0.85169,,0.50894,,16,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60450,SRR12272867,SRX8777887,SRS7048439,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_1_4.fq,fastq,511759408.0,22673361.0,C0 C0 1 4.fq.gz,0:22.57,A:100879182;C:120237907;G:142799495;T:147842595;N:229,22,,,,100879182,120237907,142799495,147842595,229,SRX8777887,SRS7048439,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83904,,0.0823,,0.84741,,0.49929,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures
60496,SRR12328853,SRX8829078,SRS7048444,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C2_C2_2_4_1.fq.gz C2_C2_2_4_2.fq.gz,fastq fastq,6974294600.0,69742946.0,C2 C2 2 4 1.fq.gz,0:100 1:100,A:2057162032;C:1418016219;G:1425580374;T:2073535975;N:0,100,100,,,2057162032,1418016219,1425580374,2073535975,0,SRX8829078,SRS7048444,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93171,,0.17455,,0.71626,,0.54961,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures
60497,SRR12328854,SRX8829077,SRS7048443,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz,fastq fastq,6942905200.0,69429052.0,C2 C2 1 4 1.fq.gz,0:100 1:100,A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0,100,100,,,2025129308,1433430820,1434784226,2049560846,0,SRX8829077,SRS7048443,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93211,,0.16662,,0.71001,,0.53674,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures
60498,SRR12328855,SRX8829076,SRS7048442,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz,fastq fastq,6973657600.0,69736576.0,C1 C1 2 4 1.fq.gz,0:100 1:100,A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0,100,100,,,2050440259,1423350359,1423015668,2076851314,0,SRX8829076,SRS7048442,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.92911,,0.1877,,0.72025,,0.58085,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures
60499,SRR12328856,SRX8829075,SRS7048441,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz,fastq fastq,6746729200.0,67467292.0,C1 C1 1 4 1.fq.gz,0:100 1:100,A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0,100,100,,,2004203843,1356765594,1357760526,2027999237,0,SRX8829075,SRS7048441,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.92733,,0.19903,,0.72228,,0.59259,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures
60500,SRR12328857,SRX8829074,SRS7048440,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz,fastq fastq,6924724800.0,69247248.0,C0 C0 2 4 1.fq.gz,0:100 1:100,A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0,100,100,,,1974618038,1471821932,1482725702,1995559128,0,SRX8829074,SRS7048440,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93473,,0.14676,,0.69649,,0.50413,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures
60501,SRR12328858,SRX8829073,SRS7048439,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz,fastq fastq,6899505600.0,68995056.0,C0 C0 1 4 1.fq.gz,0:100 1:100,A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0,100,100,,,1957459931,1477351919,1482435319,1982258431,0,SRX8829073,SRS7048439,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93567,,0.14057,,0.6883,,0.48707,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures
60550,SRR12342828,SRX8842536,SRS7105601,SRP274071,PRJNA649399,zebrafish 5 dpf sequencing,PRJNA649399,Other,For a more comprehensive analysis for the role of oxr1a on zebrafish for protection against oxidative stress,,,,,WT CTRL,,strain:no|isolate:without|breed:AB line|cultivar:1|ecotype:2|age:5 dpf|dev stage:larval|sex:male|tissue:whole fish|BioSampleModel:Model organism or animal,,,,,,,,,whole fish,729729,729729,AB line gene knockout,,,WGS,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP274071,,,WT_ctrl1 WT_ctrl2,fastq fastq,2795932250.0,11183729.0,WT ctrl1.gz,0:125 1:125,A:714170507;C:687382036;G:684930011;T:709446720;N:2976,125,125,,,714170507,687382036,684930011,709446720,2976,SRX8842536,SRS7105601,SRA1105186,Southwest University|College of Animal Science and Technolgoy,Southwest University,2,0.96284,0.9622,0.06398,0.06785,0.70276,0.70179,0.50363,0.50583,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-29,Larval,Larval,Whole Organism,All anatomical structures
62699,SRR13320609,SRX9748089,SRS7936232,SRP299308,PRJNA688414,WT and oxr1b mutant zebrafish sequencing,PRJNA688414,Other,To clarify the role of oxr1b in regulating genome wide gene expression during early oxidative stress response  the comparative transcriptome analysis of WT and oxr1b /  mutant zebrafish larvae were performed by RNA seq.,,,,danio rerio,zebrafish larval,,strain:AB line|isolate:n1|breed:wt type and mutant|cultivar:no|ecotype:Chongqing|age:5 dpf|dev stage:larval stage|sex:not collected|tissue:whole fish|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptome Analysis the Early Molecular Response of Oxr1b /  Mutant Zebrafish Larvae to Oxidative Stress by RNA Seq,MJ20201107019,MJ20201107019,The total RNA samples were isolated from WT and oxr1b /  mutant zebrafish larvae by the RNAiso Plus kit,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP299308,,,WT_H2O2.R1.fastq.gz WT_H2O2.R2.fastq.gz WT_ctrl.R1.fastq.gz WT_ctrl.R2.fastq.gz moxr1b_H2O2.R1.fastq.gz moxr1b_H2O2.R2.fastq.gz moxr1b_ctrl.R1.fastq.gz moxr1b_ctrl.R2.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,30986524572.0,102604386.0,WT H2O2.R1.fastq.gz,0:151 1:151,A:8204027517;C:7238523175;G:7419111448;T:8124456513;N:405919,151,151,,,8204027517,7238523175,7419111448,8124456513,405919,SRX9748089,SRS7936232,SRA1178651,Southwest University|College of Fisheries,Southwest University,2,0.94082,0.91236,0.08994,0.08673,0.65997,0.66478,0.48105,0.48139,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-12-29,Larval,Larval,Whole Organism,All anatomical structures
64161,SRR14308450,SRX10663886,SRS8758306,SRP315996,PRJNA724011,BDE 47 zebrafish 24hpf 4dpf,PRJNA724011,Other,,,,,,D1,,strain:AB10|age:24hpf10|dev stage:24hpf10|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal,,,,,,,,,AB10,L10,L10,paried end seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP315996,,,D1.raw_1.fastq.gz D1.raw_2.fastq.gz,fastq fastq,6493890000.0,21646300.0,D1.raw 1.fastq.gz,0:150 1:150,A:1744755708;C:1484305355;G:1549325281;T:1715269253;N:234403,150,150,,,1744755708,1484305355,1549325281,1715269253,234403,SRX10663886,SRS8758306,SRA1222808,Shantou University|Medical Colleg,Shantou University,2,0.94046,0.93893,0.09092,0.08953,0.69179,0.6957,0.47163,0.4711,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-04-27,Pharyngula,Embryo,Whole Organism,All anatomical structures
64163,SRR14308452,SRX10663884,SRS8758304,SRP315996,PRJNA724011,BDE 47 zebrafish 24hpf 4dpf,PRJNA724011,Other,,,,,,C2,,strain:AB8|age:24hpf8|dev stage:24hpf8|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal,,,,,,,,,AB8,L8,L8,paried end seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP315996,,,C2.raw_1.fastq.gz C2.raw_2.fastq.gz,fastq fastq,5887783500.0,19625945.0,C2.raw 1.fastq.gz,0:150 1:150,A:1539979565;C:1392825547;G:1451253488;T:1503541801;N:183099,150,150,,,1539979565,1392825547,1451253488,1503541801,183099,SRX10663884,SRS8758304,SRA1222808,Shantou University|Medical Colleg,Shantou University,2,0.94543,0.94466,0.06666,0.06614,0.73342,0.73468,0.46413,0.46432,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-04-27,Pharyngula,Embryo,Whole Organism,All anatomical structures
64164,SRR14308453,SRX10663883,SRS8758303,SRP315996,PRJNA724011,BDE 47 zebrafish 24hpf 4dpf,PRJNA724011,Other,,,,,,C1,,strain:AB7|age:24hpf7|dev stage:24hpf7|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal,,,,,,,,,AB7,L7,L7,paried end seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP315996,,,C1.raw_1.fastq.gz C1.raw_2.fastq.gz,fastq fastq,5878215900.0,19594053.0,C1.raw 1.fastq.gz,0:150 1:150,A:1567876584;C:1356626287;G:1407943115;T:1545550803;N:219111,150,150,,,1567876584,1356626287,1407943115,1545550803,219111,SRX10663883,SRS8758303,SRA1222808,Shantou University|Medical Colleg,Shantou University,2,0.93508,0.93337,0.08056,0.08002,0.74024,0.74276,0.47159,0.47142,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-04-27,Pharyngula,Embryo,Whole Organism,All anatomical structures
64165,SRR14308454,SRX10663882,SRS8758302,SRP315996,PRJNA724011,BDE 47 zebrafish 24hpf 4dpf,PRJNA724011,Other,,,,,,B3,,strain:AB6|age:24hpf6|dev stage:24hpf6|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal,,,,,,,,,AB6,L6,L6,paried end seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP315996,,,B3.raw_1.fastq.gz B3.raw_2.fastq.gz,fastq fastq,5684530200.0,18948434.0,B3.raw 1.fastq.gz,0:150 1:150,A:1468959527;C:1362254368;G:1409533547;T:1443570573;N:212185,150,150,,,1468959527,1362254368,1409533547,1443570573,212185,SRX10663882,SRS8758302,SRA1222808,Shantou University|Medical Colleg,Shantou University,2,0.74739,0.74464,0.07384,0.07335,0.72671,0.72977,0.46742,0.47358,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-04-27,Pharyngula,Embryo,Whole Organism,All anatomical structures
64166,SRR14308455,SRX10663881,SRS8758301,SRP315996,PRJNA724011,BDE 47 zebrafish 24hpf 4dpf,PRJNA724011,Other,,,,,,B2,,strain:AB5|age:24hpf5|dev stage:24hpf5|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal,,,,,,,,,AB5,L5,L5,paried end seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP315996,,,B2.raw_1.fastq.gz B2.raw_2.fastq.gz,fastq fastq,6605542500.0,22018475.0,B2.raw 1.fastq.gz,0:150 1:150,A:1776549620;C:1511937358;G:1570716255;T:1746097273;N:241994,150,150,,,1776549620,1511937358,1570716255,1746097273,241994,SRX10663881,SRS8758301,SRA1222808,Shantou University|Medical Colleg,Shantou University,2,0.94479,0.94309,0.09199,0.09117,0.7024,0.70445,0.46871,0.46925,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-04-27,Pharyngula,Embryo,Whole Organism,All anatomical structures
64167,SRR14308456,SRX10663880,SRS8758300,SRP315996,PRJNA724011,BDE 47 zebrafish 24hpf 4dpf,PRJNA724011,Other,,,,,,B1,,strain:AB4|age:24hpf4|dev stage:24hpf4|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal,,,,,,,,,AB4,L4,L4,paried end seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP315996,,,B1.raw_1.fastq.gz B1.raw_2.fastq.gz,fastq fastq,5853655500.0,19512185.0,B1.raw 1.fastq.gz,0:150 1:150,A:1571488140;C:1342134462;G:1393752149;T:1546065949;N:214800,150,150,,,1571488140,1342134462,1393752149,1546065949,214800,SRX10663880,SRS8758300,SRA1222808,Shantou University|Medical Colleg,Shantou University,2,0.94318,0.94153,0.08642,0.08621,0.7024,0.70508,0.46359,0.46397,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2021-04-27,Pharyngula,Embryo,Whole Organism,All anatomical structures