{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"smartseq\" and tissue_curation = \"Whole Organism\"", "rows": [[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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "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", null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, null, null, null, null, null, null, null, "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 \u03bcm 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/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae 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", null, "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, null, null, 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", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50527, "SRR8129710", "SRX4950832", "SRS3993023", "SRP167139", "PRJNA499073", "Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes", "GSE121917", "Transcriptome Analysis", "We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.", null, "pubmed:30894119", null, "Rneasy unsorted", "GSM3449971", null, "tissue:Fli:GFP  whole embryo 5 days  RNeasy  sample 1|cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNeasy plus micro kit", "Rneasy unsorted", "Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data", "Fli:GFP  whole embryo 5 days  RNeasy  sample 1", null, "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", null, "cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNeasy plus micro kit", "GSM3449971", "GSM3449971: Rneasy unsorted; Danio rerio; RNA Seq", "GSM3449971", null, "1", "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", "GEO Accession:GSM3449971", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP167139", null, null, "Q_unsorted_R1.fastq.gz Q_unsorted_R2.fastq.gz", "fastq fastq", 4155128139.0, 27505173.0, "GSM3449971 r1", "0:75.53 1:75.53", "A:1075371555;C:1005905830;G:1019395949;T:1054443500;N:11305", 75, 75, null, null, 1075371555, 1005905830, 1019395949, 1054443500, 11305, "SRX4950832", "SRS3993023", "SRA800291", "GEO", "Center for Medical Genetics, Ghent University", 2, 0.92688, 0.92569, 0.06942, 0.0708, 0.73241, 0.74164, 0.44144, 0.44652, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2018-10-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [50528, "SRR8129709", "SRX4950831", "SRS3993022", "SRP167139", "PRJNA499073", "Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes", "GSE121917", "Transcriptome Analysis", "We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.", null, "pubmed:30894119", null, "RNAqueous unsorted", "GSM3449970", null, "tissue:Fli:GFP  whole embryo 5 days  RNAqueous  sample 1|cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNAqueous micro", "RNAqueous unsorted", "Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data", "Fli:GFP  whole embryo 5 days  RNAqueous  sample 1", null, "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", null, "cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNAqueous micro", "GSM3449970", "GSM3449970: RNAqueous unsorted; Danio rerio; RNA Seq", "GSM3449970", null, "1", "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", "GEO Accession:GSM3449970", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP167139", null, null, "A_unsorted_R1.fastq.gz A_unsorted_R2.fastq.gz", "fastq fastq", 3613198121.0, 23920751.0, "GSM3449970 r1", "0:75.53 1:75.52", "A:976322858;C:832409562;G:835538411;T:968916959;N:10331", 75, 75, null, null, 976322858, 832409562, 835538411, 968916959, 10331, "SRX4950831", "SRS3993022", "SRA800291", "GEO", "Center for Medical Genetics, Ghent University", 2, 0.91518, 0.91772, 0.12399, 0.12715, 0.71196, 0.71764, 0.46555, 0.45805, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2018-10-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55867, "SRR10863009", "SRX7533060", "SRS5972251", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 10dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:10dpf|dev stage:larval|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 10dpf", "imb ketting 2018 18 redl SmartSeq2 05 10dpf PGCs rep3 S22", "imb ketting 2018 18 redl SmartSeq2 05 10dpf PGCs rep3 S22", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-05_10dpf_PGCs_rep3_S22.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-05_10dpf_PGCs_rep3_S22.R2.fastq.gz", "fastq fastq", 2398956750.0, 15993045.0, "imb ketting 2018 18 redl SmartSeq2 05 10dpf PGCs rep3 S22.R1.fastq.gz", "0:75 1:75", "A:644406123;C:549461993;G:551876029;T:653190800;N:21805", 75, 75, null, null, 644406123, 549461993, 551876029, 653190800, 21805, "SRX7533060", "SRS5972251", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93212, 0.93465, 0.08119, 0.0809, 0.64924, 0.65273, 0.49088, 0.48853, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55868, "SRR10863010", "SRX7533059", "SRS5972250", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 10dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:10dpf|dev stage:larval|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 10dpf", "imb ketting 2018 18 redl SmartSeq2 04 10dpf PGCs rep2 S21", "imb ketting 2018 18 redl SmartSeq2 04 10dpf PGCs rep2 S21", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-04_10dpf_PGCs_rep2_S21.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-04_10dpf_PGCs_rep2_S21.R2.fastq.gz", "fastq fastq", 1718401350.0, 11456009.0, "imb ketting 2018 18 redl SmartSeq2 04 10dpf PGCs rep2 S21.R1.fastq.gz", "0:75 1:75", "A:458124712;C:395812381;G:396455319;T:467992998;N:15940", 75, 75, null, null, 458124712, 395812381, 396455319, 467992998, 15940, "SRX7533059", "SRS5972250", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.9304, 0.93343, 0.06159, 0.06103, 0.6648, 0.66778, 0.4903, 0.48931, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55869, "SRR10863011", "SRX7533058", "SRS5972249", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 10dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:10dpf|dev stage:larval|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 10dpf", "imb ketting 2018 18 redl SmartSeq2 03 10dpf PGCs rep1 S20", "imb ketting 2018 18 redl SmartSeq2 03 10dpf PGCs rep1 S20", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-03_10dpf_PGCs_rep1_S20.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-03_10dpf_PGCs_rep1_S20.R2.fastq.gz", "fastq fastq", 2233099350.0, 14887329.0, "imb ketting 2018 18 redl SmartSeq2 03 10dpf PGCs rep1 S20.R1.fastq.gz", "0:75 1:75", "A:593248327;C:517482903;G:517558773;T:604789107;N:20240", 75, 75, null, null, 593248327, 517482903, 517558773, 604789107, 20240, "SRX7533058", "SRS5972249", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93341, 0.93608, 0.06727, 0.06743, 0.65202, 0.65518, 0.48494, 0.48863, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55870, "SRR10863012", "SRX7533057", "SRS5972247", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 6dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 6dpf", "imb ketting 2018 02 redl SmartSeq 11 16 6dpf PGCs rep2 S11", "imb ketting 2018 02 redl SmartSeq 11 16 6dpf PGCs rep2 S11", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_11_16_6dpf_PGCs_rep2_S11.R2.fastq.gz imb_ketting_2018_02_redl_SmartSeq_11_16_6dpf_PGCs_rep2_S11.R1.fastq.gz", "fastq fastq", 3073587588.0, 19453086.0, "imb ketting 2018 02 redl SmartSeq 11 16 6dpf PGCs rep2 S11.R1.fastq.gz", "0:79 1:79", "A:818976238;C:715663048;G:701056981;T:837683663;N:207658", 79, 79, null, null, 818976238, 715663048, 701056981, 837683663, 207658, "SRX7533057", "SRS5972247", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93657, 0.93564, 0.07313, 0.07324, 0.66732, 0.66927, 0.51839, 0.51879, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55871, "SRR10863014", "SRX7533056", "SRS5972246", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 6dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 6dpf", "imb ketting 2018 02 redl SmartSeq 10 15 6dpf PGCs rep1 S10", "imb ketting 2018 02 redl SmartSeq 10 15 6dpf PGCs rep1 S10", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_10_15_6dpf_PGCs_rep1_S10.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_10_15_6dpf_PGCs_rep1_S10.R2.fastq.gz", "fastq fastq", 3659744204.0, 23162938.0, "imb ketting 2018 02 redl SmartSeq 10 15 6dpf PGCs rep1 S10.R1.fastq.gz", "0:79 1:79", "A:975611259;C:856115631;G:822696649;T:1005067499;N:253166", 79, 79, null, null, 975611259, 856115631, 822696649, 1005067499, 253166, "SRX7533056", "SRS5972246", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.9257, 0.92714, 0.08263, 0.08288, 0.66403, 0.66606, 0.51827, 0.51415, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55873, "SRR10863013", "SRX7533054", "SRS5972248", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 6dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 6dpf", "imb ketting 2018 02 redl SmartSeq 12 57 6dpf PGCs rep3 S12", "imb ketting 2018 02 redl SmartSeq 12 57 6dpf PGCs rep3 S12", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_12_57_6dpf_PGCs_rep3_S12.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_12_57_6dpf_PGCs_rep3_S12.R2.fastq.gz", "fastq fastq", 3238333398.0, 20495781.0, "imb ketting 2018 02 redl SmartSeq 12 57 6dpf PGCs rep3 S12.R1.fastq.gz", "0:79 1:79", "A:863266932;C:756411819;G:730470194;T:887962716;N:221737", 79, 79, null, null, 863266932, 756411819, 730470194, 887962716, 221737, "SRX7533054", "SRS5972248", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93352, 0.93414, 0.07865, 0.07846, 0.6619, 0.66365, 0.50442, 0.5037, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55874, "SRR10863016", "SRX7533053", "SRS5972245", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 3dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:3dpf|dev stage:protruding mouth|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 3dpf", "imb ketting 2018 02 redl SmartSeq 09 52 3dpf PGCs rep3 S9", "imb ketting 2018 02 redl SmartSeq 09 52 3dpf PGCs rep3 S9", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_09_52_3dpf_PGCs_rep3_S9.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_09_52_3dpf_PGCs_rep3_S9.R2.fastq.gz", "fastq fastq", 3249954930.0, 20569335.0, "imb ketting 2018 02 redl SmartSeq 09 52 3dpf PGCs rep3 S9.R1.fastq.gz", "0:79 1:79", "A:869000041;C:756586733;G:737450634;T:886691114;N:226408", 79, 79, null, null, 869000041, 756586733, 737450634, 886691114, 226408, "SRX7533053", "SRS5972245", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93775, 0.93746, 0.05915, 0.05925, 0.66559, 0.66813, 0.4987, 0.49658, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55875, "SRR10863017", "SRX7533052", "SRS5972243", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 3dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:3dpf|dev stage:protruding mouth|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 3dpf", "imb ketting 2018 02 redl SmartSeq 08 46 3dpf PGCs rep2 S8", "imb ketting 2018 02 redl SmartSeq 08 46 3dpf PGCs rep2 S8", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_08_46_3dpf_PGCs_rep2_S8.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_08_46_3dpf_PGCs_rep2_S8.R2.fastq.gz", "fastq fastq", 2750070738.0, 17405511.0, "imb ketting 2018 02 redl SmartSeq 08 46 3dpf PGCs rep2 S8.R1.fastq.gz", "0:79 1:79", "A:733848756;C:641808995;G:625301352;T:748928086;N:183549", 79, 79, null, null, 733848756, 641808995, 625301352, 748928086, 183549, "SRX7533052", "SRS5972243", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93969, 0.94099, 0.07298, 0.07296, 0.6591, 0.6608, 0.46537, 0.46521, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55876, "SRR10863018", "SRX7533051", "SRS5972242", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 3dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:3dpf|dev stage:protruding mouth|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 3dpf", "imb ketting 2018 02 redl SmartSeq 07 32 3dpf PGCs rep1 S7", "imb ketting 2018 02 redl SmartSeq 07 32 3dpf PGCs rep1 S7", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_07_32_3dpf_PGCs_rep1_S7.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_07_32_3dpf_PGCs_rep1_S7.R2.fastq.gz", "fastq fastq", 3579619086.0, 22655817.0, "imb ketting 2018 02 redl SmartSeq 07 32 3dpf PGCs rep1 S7.R1.fastq.gz", "0:79 1:79", "A:953705275;C:837082021;G:815003971;T:973585384;N:242435", 79, 79, null, null, 953705275, 837082021, 815003971, 973585384, 242435, "SRX7533051", "SRS5972242", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94105, 0.94076, 0.07884, 0.07956, 0.66046, 0.66188, 0.46606, 0.46734, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55877, "SRR10863019", "SRX7533050", "SRS5972252", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 2dpf", "imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6", "imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R2.fastq.gz", "fastq fastq", 3108720942.0, 19675449.0, "imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6.R1.fastq.gz", "0:79 1:79", "A:837919918;C:714812252;G:702998193;T:852776390;N:214189", 79, 79, null, null, 837919918, 714812252, 702998193, 852776390, 214189, "SRX7533050", "SRS5972252", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93952, 0.93945, 0.07277, 0.07278, 0.66983, 0.67221, 0.50192, 0.50133, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55878, "SRR10863020", "SRX7533049", "SRS5972244", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 2dpf", "imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5", "imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R2.fastq.gz", "fastq fastq", 3241530370.0, 20516015.0, "imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5.R1.fastq.gz", "0:79 1:79", "A:861911078;C:762577918;G:730686512;T:886132359;N:222503", 79, 79, null, null, 861911078, 762577918, 730686512, 886132359, 222503, "SRX7533049", "SRS5972244", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93797, 0.93734, 0.06416, 0.06415, 0.67004, 0.67251, 0.50367, 0.50353, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55879, "SRR10863021", "SRX7533048", "SRS5972269", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 2dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 2dpf", "imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4", "imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R2.fastq.gz", "fastq fastq", 3363342524.0, 21286978.0, "imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4.R1.fastq.gz", "0:79 1:79", "A:906938869;C:772810568;G:756589497;T:926768184;N:235406", 79, 79, null, null, 906938869, 772810568, 756589497, 926768184, 235406, "SRX7533048", "SRS5972269", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93588, 0.93667, 0.11457, 0.11483, 0.66663, 0.66799, 0.4795, 0.4762, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55880, "SRR10863022", "SRX7533047", "SRS5972268", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 1dpf", "imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3", "imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R2.fastq.gz", "fastq fastq", 3406105382.0, 21557629.0, "imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3.R1.fastq.gz", "0:79 1:79", "A:914561772;C:790081165;G:768217890;T:933018206;N:226349", 79, 79, null, null, 914561772, 790081165, 768217890, 933018206, 226349, "SRX7533047", "SRS5972268", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93859, 0.93927, 0.06346, 0.06362, 0.68467, 0.68665, 0.51016, 0.44765, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55881, "SRR10863023", "SRX7533046", "SRS5972267", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 1dpf", "imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2", "imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R2.fastq.gz", "fastq fastq", 3126220074.0, 19786203.0, "imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2.R1.fastq.gz", "0:79 1:79", "A:835660285;C:727271703;G:711392935;T:851683391;N:211760", 79, 79, null, null, 835660285, 727271703, 711392935, 851683391, 211760, "SRX7533046", "SRS5972267", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93836, 0.93845, 0.05796, 0.0579, 0.67805, 0.68002, 0.49555, 0.49733, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55885, "SRR10863024", "SRX7533042", "SRS5972265", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: PGCs 1dpf", "imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1", "imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R2.fastq.gz", "fastq fastq", 3512354852.0, 22230094.0, "imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1.R1.fastq.gz", "0:79 1:79", "A:937439392;C:820724988;G:797835842;T:956108725;N:245905", 79, 79, null, null, 937439392, 820724988, 797835842, 956108725, 245905, "SRX7533042", "SRS5972265", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94053, 0.94062, 0.05733, 0.05792, 0.6801, 0.68174, 0.49423, 0.49408, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55886, "SRR10863027", "SRX7533041", "SRS5972266", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 10dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:10dpf|dev stage:larval|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 10dpf", "imb ketting 2018 18 redl SmartSeq2 02 10dpf fish rep2 S19", "imb ketting 2018 18 redl SmartSeq2 02 10dpf fish rep2 S19", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-02_10dpf_fish_rep2_S19.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-02_10dpf_fish_rep2_S19.R2.fastq.gz", "fastq fastq", 2625890700.0, 17505938.0, "imb ketting 2018 18 redl SmartSeq2 02 10dpf fish rep2 S19.R1.fastq.gz", "0:75 1:75", "A:702642659;C:603804487;G:604515055;T:714904148;N:24351", 75, 75, null, null, 702642659, 603804487, 604515055, 714904148, 24351, "SRX7533041", "SRS5972266", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.93546, 0.93678, 0.11349, 0.11316, 0.67829, 0.68217, 0.45966, 0.46585, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55888, "SRR10863029", "SRX7533039", "SRS5972264", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 10dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:10dpf|dev stage:larval|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 10dpf", "imb ketting 2018 18 redl SmartSeq2 01 10dpf fish rep1 S18", "imb ketting 2018 18 redl SmartSeq2 01 10dpf fish rep1 S18", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-01_10dpf_fish_rep1_S18.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-01_10dpf_fish_rep1_S18.R2.fastq.gz", "fastq fastq", 2317008450.0, 15446723.0, "imb ketting 2018 18 redl SmartSeq2 01 10dpf fish rep1 S18.R1.fastq.gz", "0:75 1:75", "A:616522892;C:537227364;G:538867346;T:624369327;N:21521", 75, 75, null, null, 616522892, 537227364, 538867346, 624369327, 21521, "SRX7533039", "SRS5972264", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94141, 0.94282, 0.09767, 0.09803, 0.67771, 0.68081, 0.46229, 0.46273, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55889, "SRR10863030", "SRX7533038", "SRS5972263", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 6dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 6dpf", "imb ketting 2018 02 redl SmartSeq 20 67 6dpf Fish rep2 S20", "imb ketting 2018 02 redl SmartSeq 20 67 6dpf Fish rep2 S20", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_20_67_6dpf_Fish_rep2_S20.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_20_67_6dpf_Fish_rep2_S20.R2.fastq.gz", "fastq fastq", 3141146018.0, 19880671.0, "imb ketting 2018 02 redl SmartSeq 20 67 6dpf Fish rep2 S20.R1.fastq.gz", "0:79 1:79", "A:838842352;C:731410784;G:716864447;T:853811876;N:216559", 79, 79, null, null, 838842352, 731410784, 716864447, 853811876, 216559, "SRX7533038", "SRS5972263", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94189, 0.94199, 0.11104, 0.11083, 0.68787, 0.68976, 0.4417, 0.44175, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55890, "SRR10863031", "SRX7533037", "SRS5972262", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 6dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:6dpf|dev stage:larval|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 6dpf", "imb ketting 2018 02 redl SmartSeq 19 66 6dpf Fish rep1 S19", "imb ketting 2018 02 redl SmartSeq 19 66 6dpf Fish rep1 S19", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_19_66_6dpf_Fish_rep1_S19.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_19_66_6dpf_Fish_rep1_S19.R2.fastq.gz", "fastq fastq", 3208247986.0, 20305367.0, "imb ketting 2018 02 redl SmartSeq 19 66 6dpf Fish rep1 S19.R1.fastq.gz", "0:79 1:79", "A:854547229;C:748854314;G:732176934;T:872455301;N:214208", 79, 79, null, null, 854547229, 748854314, 732176934, 872455301, 214208, "SRX7533037", "SRS5972262", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.9405, 0.94167, 0.1138, 0.1145, 0.67858, 0.683, 0.46082, 0.42095, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55891, "SRR10863032", "SRX7533036", "SRS5972261", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 3dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:3dpf|dev stage:protruding mouth|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 3dpf", "imb ketting 2018 02 redl SmartSeq 18 68 3dpf Fish rep2 S18", "imb ketting 2018 02 redl SmartSeq 18 68 3dpf Fish rep2 S18", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_18_68_3dpf_Fish_rep2_S18.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_18_68_3dpf_Fish_rep2_S18.R2.fastq.gz", "fastq fastq", 3473912978.0, 21986791.0, "imb ketting 2018 02 redl SmartSeq 18 68 3dpf Fish rep2 S18.R1.fastq.gz", "0:79 1:79", "A:926028590;C:808989307;G:800996495;T:937660664;N:237922", 79, 79, null, null, 926028590, 808989307, 800996495, 937660664, 237922, "SRX7533036", "SRS5972261", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94661, 0.94606, 0.09208, 0.09205, 0.67896, 0.68105, 0.43418, 0.44149, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55892, "SRR10863033", "SRX7533035", "SRS5972260", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 3dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:3dpf|dev stage:protruding mouth|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 3dpf", "imb ketting 2018 02 redl SmartSeq 17 03 3dpf Fish rep1 S17", "imb ketting 2018 02 redl SmartSeq 17 03 3dpf Fish rep1 S17", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_17_03_3dpf_Fish_rep1_S17.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_17_03_3dpf_Fish_rep1_S17.R2.fastq.gz", "fastq fastq", 3383193960.0, 21412620.0, "imb ketting 2018 02 redl SmartSeq 17 03 3dpf Fish rep1 S17.R1.fastq.gz", "0:79 1:79", "A:903658559;C:789740630;G:763902271;T:925656543;N:235957", 79, 79, null, null, 903658559, 789740630, 763902271, 925656543, 235957, "SRX7533035", "SRS5972260", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94068, 0.94162, 0.11921, 0.11989, 0.67377, 0.67572, 0.45353, 0.44698, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [55893, "SRR10863034", "SRX7533034", "SRS5972259", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 2dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 2dpf", "imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16", "imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R2.fastq.gz", "fastq fastq", 3091658206.0, 19567457.0, "imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16.R1.fastq.gz", "0:79 1:79", "A:818837054;C:727836511;G:707557580;T:837216941;N:210120", 79, 79, null, null, 818837054, 727836511, 707557580, 837216941, 210120, "SRX7533034", "SRS5972259", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94667, 0.94646, 0.08702, 0.08692, 0.69804, 0.70138, 0.43628, 0.43409, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55894, "SRR10863035", "SRX7533033", "SRS5972258", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 2dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 2dpf", "imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15", "imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R2.fastq.gz", "fastq fastq", 3499876328.0, 22151116.0, "imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15.R1.fastq.gz", "0:79 1:79", "A:931187812;C:820606968;G:796104654;T:951733888;N:243006", 79, 79, null, null, 931187812, 820606968, 796104654, 951733888, 243006, "SRX7533033", "SRS5972258", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94532, 0.94537, 0.10394, 0.10459, 0.69489, 0.69727, 0.4345, 0.43676, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [55895, "SRR10863036", "SRX7533032", "SRS5972257", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 1dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 1dpf", "imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14", "imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R2.fastq.gz", "fastq fastq", 3173577572.0, 20085934.0, "imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14.R1.fastq.gz", "0:79 1:79", "A:851665093;C:736131084;G:718748661;T:866816699;N:216035", 79, 79, null, null, 851665093, 736131084, 718748661, 866816699, 216035, "SRX7533032", "SRS5972257", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94469, 0.9439, 0.08631, 0.08612, 0.71062, 0.71204, 0.46629, 0.46237, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55896, "SRR10863037", "SRX7533031", "SRS5972256", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt Fish 1dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: Fish 1dpf", "imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13", "imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R2.fastq.gz", "fastq fastq", 3241792492.0, 20517674.0, "imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13.R1.fastq.gz", "0:79 1:79", "A:865936682;C:756362974;G:735614291;T:883655547;N:222998", 79, 79, null, null, 865936682, 756362974, 735614291, 883655547, 222998, "SRX7533031", "SRS5972256", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94544, 0.94715, 0.08154, 0.0819, 0.70928, 0.71011, 0.45932, 0.46165, 79, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55897, "SRR10863038", "SRX7533030", "SRS5972255", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt zygote 0hpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:0hpf|dev stage:zygote|sex:not applicable|tissue:whole embryo|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: zygotes 0hpf", "imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25", "imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-08_0hpf_zygotes_rep3_S25.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-08_0hpf_zygotes_rep3_S25.R2.fastq.gz", "fastq fastq", 2254742850.0, 15031619.0, "imb ketting 2018 18 redl SmartSeq2 08 0hpf zygotes rep3 S25.R1.fastq.gz", "0:75 1:75", "A:601169757;C:521134633;G:522514682;T:609902670;N:21108", 75, 75, null, null, 601169757, 521134633, 522514682, 609902670, 21108, "SRX7533030", "SRS5972255", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94461, 0.94575, 0.01803, 0.01807, 0.76751, 0.76883, 0.49585, 0.49808, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [55899, "SRR10863040", "SRX7533028", "SRS5972254", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt zygote 0hpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:0hpf|dev stage:zygote|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: zygotes 0hpf", "imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24", "imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-07_0hpf_zygotes_rep2_S24.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-07_0hpf_zygotes_rep2_S24.R2.fastq.gz", "fastq fastq", 2415051600.0, 16100344.0, "imb ketting 2018 18 redl SmartSeq2 07 0hpf zygotes rep2 S24.R1.fastq.gz", "0:75 1:75", "A:644001016;C:558385744;G:560491907;T:652150600;N:22333", 75, 75, null, null, 644001016, 558385744, 560491907, 652150600, 22333, "SRX7533028", "SRS5972254", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.9462, 0.94755, 0.02097, 0.02075, 0.76694, 0.76909, 0.4948, 0.49938, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [55900, "SRR10863041", "SRX7533027", "SRS5972253", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt zygote 0hpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:0hpf|dev stage:zygote|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA of Zebrafish: zygotes 0hpf", "imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23", "imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23", "Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_18_redl_SmartSeq2-06_0hpf_zygotes_rep1_S23.R1.fastq.gz imb_ketting_2018_18_redl_SmartSeq2-06_0hpf_zygotes_rep1_S23.R2.fastq.gz", "fastq fastq", 2621759100.0, 17478394.0, "imb ketting 2018 18 redl SmartSeq2 06 0hpf zygotes rep1 S23.R1.fastq.gz", "0:75 1:75", "A:697302326;C:607756156;G:612217195;T:704460378;N:23045", 75, 75, null, null, 697302326, 607756156, 612217195, 704460378, 23045, "SRX7533027", "SRS5972253", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 2, 0.94882, 0.95052, 0.02124, 0.02139, 0.77082, 0.7724, 0.49237, 0.49259, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2020-01-10", "Zygote", "Embryo", "Whole Organism", "All anatomical structures"], [59113, "SRR11684017", "SRX8244820", "SRS6592457", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "csf1r doubleknockout3 50hpf", "GSM4512709", null, "tissue:whole embryos|developmental stage:50 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "csf1r doubleknockout3 50hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:50 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512709", "GSM4512709: csf1r doubleknockout3 50hpf; Danio rerio; RNA Seq", "GSM4512709", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512709", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "csf1r_doubleknockout3_50hpf.bam", "bam", 2573933906.0, 17004980.0, "GSM4512709 r1", "0:75.96 1:75.40", "A:724577130;C:562040116;G:565021490;T:709993494;N:12301676", 75, 75, null, null, 724577130, 562040116, 565021490, 709993494, 12301676, "SRX8244820", "SRS6592457", "SRA1072139", "GEO", "Erasmus MC", 2, 0.9212, 0.92945, 0.13582, 0.13902, 0.77047, 0.76887, 0.4614, 0.46066, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59114, "SRR11684016", "SRX8244819", "SRS6592456", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "csf1r doubleknockout2 50hpf", "GSM4512708", null, "tissue:whole embryos|developmental stage:50 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "csf1r doubleknockout2 50hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:50 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512708", "GSM4512708: csf1r doubleknockout2 50hpf; Danio rerio; RNA Seq", "GSM4512708", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512708", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "csf1r_doubleknockout2_50hpf.bam", "bam", 2464956528.0, 16273518.0, "GSM4512708 r1", "0:75.96 1:75.51", "A:693859812;C:538765618;G:541651658;T:678953708;N:11725732", 75, 75, null, null, 693859812, 538765618, 541651658, 678953708, 11725732, "SRX8244819", "SRS6592456", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92032, 0.93082, 0.12855, 0.13111, 0.78161, 0.78169, 0.45908, 0.4613, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59115, "SRR11684015", "SRX8244818", "SRS6592455", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "csf1r doubleknockout1 50hpf", "GSM4512707", null, "tissue:whole embryos|developmental stage:50 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "csf1r doubleknockout1 50hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:50 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512707", "GSM4512707: csf1r doubleknockout1 50hpf; Danio rerio; RNA Seq", "GSM4512707", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512707", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "csf1r_doubleknockout1_50hpf.bam", "bam", 2395164160.0, 15792871.0, "GSM4512707 r1", "0:75.97 1:75.70", "A:687540528;C:509569578;G:511585096;T:674949069;N:11519889", 75, 75, null, null, 687540528, 509569578, 511585096, 674949069, 11519889, "SRX8244818", "SRS6592455", "SRA1072139", "GEO", "Erasmus MC", 2, 0.90906, 0.91851, 0.22507, 0.23023, 0.76055, 0.75929, 0.4588, 0.46776, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59116, "SRR11684014", "SRX8244817", "SRS6592454", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "wildtype cntr3 50hpf", "GSM4512706", null, "tissue:whole embryos|developmental stage:50 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "wildtype cntr3 50hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:50 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512706", "GSM4512706: wildtype cntr3 50hpf; Danio rerio; RNA Seq", "GSM4512706", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512706", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "wildtype_cntr3_50hpf.bam", "bam", 2870452960.0, 18993629.0, "GSM4512706 r1", "0:75.96 1:75.17", "A:802347034;C:632735913;G:637053428;T:784477655;N:13838930", 75, 75, null, null, 802347034, 632735913, 637053428, 784477655, 13838930, "SRX8244817", "SRS6592454", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92809, 0.93616, 0.12277, 0.1259, 0.77266, 0.77246, 0.46307, 0.46014, 76, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59117, "SRR11684013", "SRX8244816", "SRS6592453", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "wildtype cntr2 50hpf", "GSM4512705", null, "tissue:whole embryos|developmental stage:50 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "wildtype cntr2 50hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:50 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512705", "GSM4512705: wildtype cntr2 50hpf; Danio rerio; RNA Seq", "GSM4512705", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512705", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "wildtype_cntr2_50hpf.bam", "bam", 3827575472.0, 25330029.0, "GSM4512705 r1", "0:75.96 1:75.15", "A:1071770602;C:842076468;G:847771148;T:1047620159;N:18337095", 75, 75, null, null, 1071770602, 842076468, 847771148, 1047620159, 18337095, "SRX8244816", "SRS6592453", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92891, 0.93712, 0.12666, 0.13041, 0.7665, 0.76822, 0.46304, 0.45398, 76, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59118, "SRR11684012", "SRX8244815", "SRS6592452", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "wildtype cntr1 50hpf", "GSM4512704", null, "tissue:whole embryos|developmental stage:50 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "wildtype cntr1 50hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:50 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512704", "GSM4512704: wildtype cntr1 50hpf; Danio rerio; RNA Seq", "GSM4512704", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512704", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "wildtype_cntr1_50hpf.bam", "bam", 2865244754.0, 18951980.0, "GSM4512704 r1", "0:75.97 1:75.22", "A:804408593;C:627603063;G:631635890;T:787698117;N:13899091", 75, 75, null, null, 804408593, 627603063, 631635890, 787698117, 13899091, "SRX8244815", "SRS6592452", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92694, 0.93392, 0.1401, 0.14332, 0.76414, 0.76392, 0.44974, 0.4562, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [59119, "SRR11684011", "SRX8244814", "SRS6592451", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "csf1r doubleknockout3 28hpf", "GSM4512703", null, "tissue:whole embryos|developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "csf1r doubleknockout3 28hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512703", "GSM4512703: csf1r doubleknockout3 28hpf; Danio rerio; RNA Seq", "GSM4512703", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512703", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "csf1r_doubleknockout3_28hpf.bam", "bam", 2776983342.0, 18329912.0, "GSM4512703 r1", "0:75.96 1:75.54", "A:776587586;C:613125618;G:616153519;T:757439274;N:13677345", 75, 75, null, null, 776587586, 613125618, 616153519, 757439274, 13677345, "SRX8244814", "SRS6592451", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92512, 0.93371, 0.1054, 0.10799, 0.78307, 0.78287, 0.44838, 0.44486, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [59120, "SRR11684010", "SRX8244813", "SRS6592450", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "csf1r doubleknockout2 28hpf", "GSM4512702", null, "tissue:whole embryos|developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "csf1r doubleknockout2 28hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512702", "GSM4512702: csf1r doubleknockout2 28hpf; Danio rerio; RNA Seq", "GSM4512702", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512702", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "csf1r_doubleknockout2_28hpf.bam", "bam", 2908203540.0, 19226046.0, "GSM4512702 r1", "0:75.97 1:75.30", "A:812002267;C:642558682;G:646762399;T:792733574;N:14146618", 75, 75, null, null, 812002267, 642558682, 646762399, 792733574, 14146618, "SRX8244813", "SRS6592450", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92454, 0.93402, 0.10684, 0.11073, 0.78238, 0.78224, 0.44909, 0.44853, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [59121, "SRR11684009", "SRX8244812", "SRS6592449", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "csf1r doubleknockout1 28hpf", "GSM4512701", null, "tissue:whole embryos|developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "csf1r doubleknockout1 28hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512701", "GSM4512701: csf1r doubleknockout1 28hpf; Danio rerio; RNA Seq", "GSM4512701", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512701", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "csf1r_doubleknockout1_28hpf.bam", "bam", 1613198946.0, 10660488.0, "GSM4512701 r1", "0:75.96 1:75.37", "A:450889241;C:356351947;G:358636604;T:439481905;N:7839249", 75, 75, null, null, 450889241, 356351947, 358636604, 439481905, 7839249, "SRX8244812", "SRS6592449", "SRA1072139", "GEO", "Erasmus MC", 2, 0.92472, 0.93343, 0.10689, 0.10892, 0.77784, 0.77686, 0.45013, 0.45869, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [59122, "SRR11684008", "SRX8244811", "SRS6592448", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "wildtype cntr3 28hpf", "GSM4512700", null, "tissue:whole embryos|developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "wildtype cntr3 28hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512700", "GSM4512700: wildtype cntr3 28hpf; Danio rerio; RNA Seq", "GSM4512700", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512700", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "wildtype_cntr3_28hpf.bam", "bam", 2994589195.0, 19843035.0, "GSM4512700 r1", "0:75.96 1:74.95", "A:831532991;C:665759016;G:671898629;T:810655335;N:14743224", 75, 74, null, null, 831532991, 665759016, 671898629, 810655335, 14743224, "SRX8244811", "SRS6592448", "SRA1072139", "GEO", "Erasmus MC", 2, 0.93121, 0.93827, 0.09775, 0.09985, 0.77861, 0.77889, 0.45486, 0.4521, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [59123, "SRR11684007", "SRX8244810", "SRS6592447", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "wildtype cntr2 28hpf", "GSM4512699", null, "tissue:whole embryos|developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "wildtype cntr2 28hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512699", "GSM4512699: wildtype cntr2 28hpf; Danio rerio; RNA Seq", "GSM4512699", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512699", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "wildtype_cntr2_28hpf.bam", "bam", 2714096863.0, 17970580.0, "GSM4512699 r1", "0:75.96 1:75.07", "A:753731545;C:603594075;G:608442658;T:735104220;N:13224365", 75, 75, null, null, 753731545, 603594075, 608442658, 735104220, 13224365, "SRX8244810", "SRS6592447", "SRA1072139", "GEO", "Erasmus MC", 2, 0.93052, 0.93777, 0.09537, 0.09754, 0.7806, 0.78094, 0.45674, 0.46243, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [59124, "SRR11684006", "SRX8244809", "SRS6592446", "SRP259988", "PRJNA630160", "Zebrafish embryonic mpeg+ macrophages", "GSE149786", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "wildtype cntr1 28hpf", "GSM4512698", null, "tissue:whole embryos|developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "wildtype cntr1 28hpf", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole embryos", null, "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle", "developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512698", "GSM4512698: wildtype cntr1 28hpf; Danio rerio; RNA Seq", "GSM4512698", null, "1", "35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512698", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259988", null, "intentional duplicate", "wildtype_cntr1_28hpf.bam", "bam", 2326310736.0, 15392307.0, "GSM4512698 r1", "0:75.96 1:75.18", "A:647113553;C:516650373;G:520662730;T:630666248;N:11217832", 75, 75, null, null, 647113553, 516650373, 520662730, 630666248, 11217832, "SRX8244809", "SRS6592446", "SRA1072139", "GEO", "Erasmus MC", 2, 0.93181, 0.93856, 0.09723, 0.10044, 0.77333, 0.77285, 0.45198, 0.45136, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [59131, "SRR11684032", "SRX8244835", "SRS6592471", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo il34 3", "GSM4512724", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:il34re03/re03 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo il34 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:il34re03/re03 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512724", "GSM4512724: 5mo il34 3; Danio rerio; RNA Seq", "GSM4512724", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512724", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_il34_3_R2.fastq.gz 5mo_il34_3_R1.fastq.gz", "fastq fastq", 2866393332.0, 14190066.0, "GSM4512724 r1", "0:101 1:101", "A:820325277;C:598942699;G:621845494;T:825272271;N:7591", 101, 101, null, null, 820325277, 598942699, 621845494, 825272271, 7591, "SRX8244835", "SRS6592471", "SRA1072140", "GEO", "Erasmus MC", 2, 0.91456, 0.88642, 0.16807, 0.16787, 0.77717, 0.78817, 0.48538, 0.47123, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59132, "SRR11684031", "SRX8244834", "SRS6592470", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo il34 2", "GSM4512723", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:il34re03/re03 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo il34 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:il34re03/re03 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512723", "GSM4512723: 5mo il34 2; Danio rerio; RNA Seq", "GSM4512723", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512723", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_il34_2_R2.fastq.gz 5mo_il34_2_R1.fastq.gz", "fastq fastq", 9358608692.0, 46329746.0, "GSM4512723 r1", "0:101 1:101", "A:2688145270;C:1936550600;G:2027452342;T:2706435131;N:25349", 101, 101, null, null, 2688145270, 1936550600, 2027452342, 2706435131, 25349, "SRX8244834", "SRS6592470", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90713, 0.87837, 0.17353, 0.17278, 0.77413, 0.78494, 0.47813, 0.45746, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59133, "SRR11684030", "SRX8244833", "SRS6592469", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo il34 1", "GSM4512722", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:il34re03/re03 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo il34 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:il34re03/re03 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512722", "GSM4512722: 5mo il34 1; Danio rerio; RNA Seq", "GSM4512722", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512722", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_il34_1_R2.fastq.gz 5mo_il34_1_R1.fastq.gz", "fastq fastq", 2301153296.0, 11391848.0, "GSM4512722 r1", "0:101 1:101", "A:654795654;C:483118243;G:496611634;T:666621412;N:6353", 101, 101, null, null, 654795654, 483118243, 496611634, 666621412, 6353, "SRX8244833", "SRS6592469", "SRA1072140", "GEO", "Erasmus MC", 2, 0.91036, 0.88104, 0.15732, 0.15536, 0.7543, 0.76355, 0.47519, 0.47489, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59134, "SRR11684029", "SRX8244832", "SRS6592467", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo csf1rdm 3", "GSM4512721", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo csf1rdm 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512721", "GSM4512721: 5mo csf1rdm 3; Danio rerio; RNA Seq", "GSM4512721", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512721", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_csf1rdm_3_R2.fastq.gz 5mo_csf1rdm_3_R1.fastq.gz", "fastq fastq", 3452649448.0, 17092324.0, "GSM4512721 r1", "0:101 1:101", "A:999459335;C:713557103;G:730450368;T:1009173875;N:8767", 101, 101, null, null, 999459335, 713557103, 730450368, 1009173875, 8767, "SRX8244832", "SRS6592467", "SRA1072140", "GEO", "Erasmus MC", 2, 0.89236, 0.86757, 0.18589, 0.18351, 0.76745, 0.77717, 0.47984, 0.48136, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59135, "SRR11684028", "SRX8244831", "SRS6592466", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo csf1rdm 2", "GSM4512720", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo csf1rdm 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512720", "GSM4512720: 5mo csf1rdm 2; Danio rerio; RNA Seq", "GSM4512720", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_csf1rdm_2_R2.fastq.gz 5mo_csf1rdm_2_R1.fastq.gz", "fastq fastq", 9868898870.0, 48855935.0, "GSM4512720 r1", "0:101 1:101", "A:2841225530;C:2066572676;G:2116298647;T:2844775713;N:26304", 101, 101, null, null, 2841225530, 2066572676, 2116298647, 2844775713, 26304, "SRX8244831", "SRS6592466", "SRA1072140", "GEO", "Erasmus MC", 2, 0.89516, 0.87542, 0.18501, 0.18252, 0.764, 0.77293, 0.47581, 0.47272, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59136, "SRR11684027", "SRX8244830", "SRS6592472", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo csf1rdm 1", "GSM4512719", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo csf1rdm 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512719", "GSM4512719: 5mo csf1rdm 1; Danio rerio; RNA Seq", "GSM4512719", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512719", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_csf1rdm_1_R2.fastq.gz 5mo_csf1rdm_1_R1.fastq.gz", "fastq fastq", 2592133084.0, 12832342.0, "GSM4512719 r1", "0:101 1:101", "A:752421497;C:536462229;G:554014038;T:749228471;N:6849", 101, 101, null, null, 752421497, 536462229, 554014038, 749228471, 6849, "SRX8244830", "SRS6592472", "SRA1072140", "GEO", "Erasmus MC", 2, 0.89674, 0.87504, 0.19407, 0.19286, 0.76266, 0.77128, 0.47136, 0.47621, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59137, "SRR11684026", "SRX8244829", "SRS6592468", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo control 3", "GSM4512718", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo control 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512718", "GSM4512718: 5mo control 3; Danio rerio; RNA Seq", "GSM4512718", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512718", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_control_3_R1.fastq.gz 5mo_control_3_R2.fastq.gz", "fastq fastq", 2900146724.0, 14357162.0, "GSM4512718 r1", "0:101 1:101", "A:836328631;C:590839440;G:610358908;T:862611563;N:8182", 101, 101, null, null, 836328631, 590839440, 610358908, 862611563, 8182, "SRX8244829", "SRS6592468", "SRA1072140", "GEO", "Erasmus MC", 2, 0.92029, 0.88055, 0.20101, 0.19762, 0.77575, 0.78843, 0.47683, 0.46576, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59138, "SRR11684025", "SRX8244828", "SRS6592465", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo control 2", "GSM4512717", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo control 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512717", "GSM4512717: 5mo control 2; Danio rerio; RNA Seq", "GSM4512717", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512717", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_control_2_R2.fastq.gz 5mo_control_2_R1.fastq.gz", "fastq fastq", 3569121840.0, 17668920.0, "GSM4512717 r1", "0:101 1:101", "A:1029586591;C:742959141;G:766068597;T:1030497700;N:9811", 101, 101, null, null, 1029586591, 742959141, 766068597, 1030497700, 9811, "SRX8244828", "SRS6592465", "SRA1072140", "GEO", "Erasmus MC", 2, 0.92823, 0.90526, 0.19813, 0.19655, 0.77386, 0.78153, 0.47798, 0.45944, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59139, "SRR11684024", "SRX8244827", "SRS6592464", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "5mo control 1", "GSM4512716", null, "tissue:whole fish|developmental stage:1 mpf 5 mpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "5mo control 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:1 mpf 5 mpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512716", "GSM4512716: 5mo control 1; Danio rerio; RNA Seq", "GSM4512716", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512716", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "5mo_control_1_R1.fastq.gz 5mo_control_1_R2.fastq.gz", "fastq fastq", 2998749792.0, 14845296.0, "GSM4512716 r1", "0:101 1:101", "A:865245738;C:611065712;G:637501234;T:884928997;N:8111", 101, 101, null, null, 865245738, 611065712, 637501234, 884928997, 8111, "SRX8244827", "SRS6592464", "SRA1072140", "GEO", "Erasmus MC", 2, 0.9234, 0.8848, 0.19688, 0.19386, 0.73285, 0.7469, 0.48735, 0.46533, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [59140, "SRR11684023", "SRX8244826", "SRS6592463", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf csf1rdm 3", "GSM4512715", null, "tissue:whole fish|developmental stage:33 dpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf csf1rdm 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512715", "GSM4512715: 33dpf csf1rdm 3; Danio rerio; RNA Seq", "GSM4512715", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512715", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_csf1rdm_3_R2.fastq.gz 33dpf_csf1rdm_3_R1.fastq.gz", "fastq fastq", 4266500984.0, 21121292.0, "GSM4512715 r1", "0:101 1:101", "A:1228176589;C:888764172;G:911251380;T:1238297282;N:11561", 101, 101, null, null, 1228176589, 888764172, 911251380, 1238297282, 11561, "SRX8244826", "SRS6592463", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90846, 0.8852, 0.18604, 0.18551, 0.77149, 0.78056, 0.47511, 0.46363, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59141, "SRR11684022", "SRX8244825", "SRS6592462", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf csf1rdm 2", "GSM4512714", null, "tissue:whole fish|developmental stage:33 dpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf csf1rdm 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512714", "GSM4512714: 33dpf csf1rdm 2; Danio rerio; RNA Seq", "GSM4512714", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512714", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_csf1rdm_2_R2.fastq.gz 33dpf_csf1rdm_2_R1.fastq.gz", "fastq fastq", 34856013646.0, 172554523.0, "GSM4512714 r1", "0:101 1:101", "A:10025368414;C:7294167881;G:7483951837;T:10052430673;N:94841", 101, 101, null, null, 10025368414, 7294167881, 7483951837, 10052430673, 94841, "SRX8244825", "SRS6592462", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90986, 0.88677, 0.1819, 0.18005, 0.7601, 0.76921, 0.48551, 0.47188, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59142, "SRR11684021", "SRX8244824", "SRS6592461", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf csf1rdm 1", "GSM4512713", null, "tissue:whole fish|developmental stage:33 dpf|strain:csf1raj4e1/j4e1; csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf csf1rdm 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512713", "GSM4512713: 33dpf csf1rdm 1; Danio rerio; RNA Seq", "GSM4512713", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512713", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_csf1rdm_1_R1.fastq.gz 33dpf_csf1rdm_1_R2.fastq.gz", "fastq fastq", 3251371598.0, 16095899.0, "GSM4512713 r1", "0:101 1:101", "A:938620484;C:677648040;G:693531098;T:941563341;N:8635", 101, 101, null, null, 938620484, 677648040, 693531098, 941563341, 8635, "SRX8244824", "SRS6592461", "SRA1072140", "GEO", "Erasmus MC", 2, 0.90369, 0.88203, 0.18089, 0.17771, 0.78234, 0.78847, 0.47498, 0.47606, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59143, "SRR11684020", "SRX8244823", "SRS6592460", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf control 3", "GSM4512712", null, "tissue:whole fish|developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf control 3", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512712", "GSM4512712: 33dpf control 3; Danio rerio; RNA Seq", "GSM4512712", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512712", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_control_3_R1.fastq.gz 33dpf_control_3_R2.fastq.gz", "fastq fastq", 2712847880.0, 13429940.0, "GSM4512712 r1", "0:101 1:101", "A:772539767;C:566195541;G:587191020;T:786914116;N:7436", 101, 101, null, null, 772539767, 566195541, 587191020, 786914116, 7436, "SRX8244823", "SRS6592460", "SRA1072140", "GEO", "Erasmus MC", 2, 0.93009, 0.89728, 0.17089, 0.17058, 0.74548, 0.75722, 0.48148, 0.47178, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59144, "SRR11684019", "SRX8244822", "SRS6592459", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf control 2", "GSM4512711", null, "tissue:whole fish|developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf control 2", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512711", "GSM4512711: 33dpf control 2; Danio rerio; RNA Seq", "GSM4512711", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512711", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_control_2_R2.fastq.gz 33dpf_control_2_R1.fastq.gz", "fastq fastq", 1740822264.0, 8617932.0, "GSM4512711 r1", "0:101 1:101", "A:496913292;C:363966331;G:377438086;T:502499900;N:4655", 101, 101, null, null, 496913292, 363966331, 377438086, 502499900, 4655, "SRX8244822", "SRS6592459", "SRA1072140", "GEO", "Erasmus MC", 2, 0.92011, 0.89184, 0.16484, 0.16269, 0.7541, 0.7655, 0.47531, 0.46847, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"], [59145, "SRR11684018", "SRX8244821", "SRS6592458", "SRP259989", "PRJNA630163", "Zebrafish juvenile mpeg+ macrophages", "GSE149787", "Transcriptome Analysis", "We used zebrafish lacking functional csf1r or il34 to unravel how and when csf1r is necessary for macrophages. Transcriptomic analysis of mpeg+ macrophages isolated from juvenile fish revealed that csf1r deficient macrophages show a gross macrophage transcriptome  but reduced expression of engulfment related genes and increased expression of genes typical for metaphocytes. Overall design: Bulk RNA sequencing of juvenile macrophages obtained from wildtype control  il34 /  and csf1rDM zebrafish triplicates", "parent bioproject:PRJNA630158", "pubmed:32367800", null, "33dpf control 1", "GSM4512710", null, "tissue:whole fish|developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "33dpf control 1", "Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks\u00a0 v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.", "whole fish", null, "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle until 5 dpf  from 5 dpf onwards in regular aquarium. Fed dry food + paramecia from 5 dpf   13 dpf. From 13 dpf onwards brine shrimps  paramecia and dry food", "developmental stage:33 dpf|strain:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells", "GSM4512710", "GSM4512710: 33dpf control 1; Danio rerio; RNA Seq", "GSM4512710", null, "1", "Single juveniles were cut in small pieces using a razor blade and dissociated with trypsin on ice for 1 hour. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4512710", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP259989", null, null, "33dpf_control_1_R2.fastq.gz 33dpf_control_1_R1.fastq.gz", "fastq fastq", 3546165954.0, 17555277.0, "GSM4512710 r1", "0:101 1:101", "A:1004040828;C:754797131;G:787411451;T:999907224;N:9320", 101, 101, null, null, 1004040828, 754797131, 787411451, 999907224, 9320, "SRX8244821", "SRS6592458", "SRA1072140", "GEO", "Erasmus MC", 2, 0.93722, 0.91292, 0.14991, 0.14981, 0.75191, 0.76171, 0.47117, 0.46955, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "trueseq", "sc", "single_cell_plate", "smartseq", null, "Netherlands", "2020-05-04", "Juvenile", "Juvenile", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 91, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "smartseq", "p2": "Whole Organism"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 63, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_selection=RANDOM+PCR", "selected": false}, {"value": "cDNA", "label": "cDNA", "count": 29, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_selection=cDNA", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_selection=PolyA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=smartseq&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "Embryo", "label": "Embryo", "count": 59, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Larval", "label": "Larval", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Juvenile", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "Pharyngula", "label": "Pharyngula", "count": 29, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Pharyngula", "selected": false}, {"value": "Larval", "label": "Larval", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Larval", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Blastula", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Hatching", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Multi-stage", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Juvenile", "selected": false}, {"value": "Segmentation", "label": "Segmentation", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Segmentation", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Zygote", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "smartseq", "label": "smartseq", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 100.3109619996394}