{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\" and experiment.library_strategy = \"OTHER\"", "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. 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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"], [25182, "SRR25670729", "SRX21396042", "SRS18636200", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA germ ring PAL seq v4", "GSM7716871", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA germ ring PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716871", "GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER", "GSM7716871 r1", "GSM7716871", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz", "fastq fastq", 2834842912.0, 9234016.0, "GSM7716871 r1", "0:52 1:255", "A:725811118;C:702410592;G:747583409;T:651018348;N:8019445", 52, 255, null, null, 725811118, 702410592, 747583409, 651018348, 8019445, "SRX21396042", "SRS18636200", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00023, 0.30494, 8e-05, 0.01793, 0.99967, 0.99971, 0.5, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25183, "SRR25670730", "SRX21396042", "SRS18636200", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA germ ring PAL seq v4", "GSM7716871", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA germ ring PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716871", "GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER", "GSM7716871 r1", "GSM7716871", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3473033898.0, 11312814.0, "GSM7716871 r2", "0:52 1:255", "A:853178471;C:899976159;G:962100712;T:750811461;N:6967095", 52, 255, null, null, 853178471, 899976159, 962100712, 750811461, 6967095, "SRX21396042", "SRS18636200", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00049, 0.0, 0.00012, 0.0, 0.99941, 1.0, 0.64864, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25184, "SRR25670731", "SRX21396041", "SRS18636199", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA zfs:0000015 PAL seq v4", "GSM7716870", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA zfs:0000015 PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716870", "GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER", "GSM7716870 r1", "GSM7716870", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2695203962.0, 8779166.0, "GSM7716870 r1", "0:52 1:255", "A:684535386;C:669852151;G:719008886;T:614209811;N:7597728", 52, 255, null, null, 684535386, 669852151, 719008886, 614209811, 7597728, "SRX21396041", "SRS18636199", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00117, 0.35837, 0.00017, 0.00682, 0.99859, 0.99963, 0.69473, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25185, "SRR25670732", "SRX21396041", "SRS18636199", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA zfs:0000015 PAL seq v4", "GSM7716870", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA zfs:0000015 PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716870", "GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER", "GSM7716870 r1", "GSM7716870", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz", "fastq fastq", 3476338446.0, 11323578.0, "GSM7716870 r2", "0:52 1:255", "A:841832234;C:898325199;G:968774318;T:760398070;N:7008625", 52, 255, null, null, 841832234, 898325199, 968774318, 760398070, 7008625, "SRX21396041", "SRS18636199", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00245, 0.0, 0.00047, 0.0, 0.99803, 1.0, 0.58536, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25186, "SRR25670733", "SRX21396040", "SRS18636198", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA sphere PAL seq v4", "GSM7716869", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA sphere PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716869", "GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER", "GSM7716869 r1", "GSM7716869", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 3211687254.0, 10461522.0, "GSM7716869 r1", "0:52 1:255", "A:813560400;C:775326762;G:854563477;T:759161458;N:9075157", 52, 255, null, null, 813560400, 775326762, 854563477, 759161458, 9075157, "SRX21396040", "SRS18636198", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00088, 0.43191, 0.0004, 0.01556, 0.99916, 0.99961, 0.55769, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25187, "SRR25670734", "SRX21396040", "SRS18636198", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA sphere PAL seq v4", "GSM7716869", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA sphere PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716869", "GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER", "GSM7716869 r1", "GSM7716869", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3179916131.0, 10358033.0, "GSM7716869 r2", "0:52 1:255", "A:771755667;C:804256300;G:883166175;T:714242073;N:6495916", 52, 255, null, null, 771755667, 804256300, 883166175, 714242073, 6495916, "SRX21396040", "SRS18636198", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00186, 0.0, 0.00088, 0.0, 0.99862, 1.0, 0.64705, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25188, "SRR25670735", "SRX21396039", "SRS18636197", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 1024cell PAL seq v4", "GSM7716868", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1024cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716868", "GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER", "GSM7716868 r1", "GSM7716868", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2191900794.0, 7139742.0, "GSM7716868 r1", "0:52 1:255", "A:571954354;C:551162617;G:572445400;T:490238669;N:6099754", 52, 255, null, null, 571954354, 551162617, 572445400, 490238669, 6099754, "SRX21396039", "SRS18636197", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0011, 0.43387, 6e-05, 0.01058, 0.99864, 0.99971, 0.74576, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25189, "SRR25670736", "SRX21396039", "SRS18636197", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 1024cell PAL seq v4", "GSM7716868", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1024cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716868", "GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER", "GSM7716868 r1", "GSM7716868", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3840723193.0, 12510499.0, "GSM7716868 r2", "0:52 1:255", "A:985340216;C:991311706;G:1034487140;T:821820974;N:7763157", 52, 255, null, null, 985340216, 991311706, 1034487140, 821820974, 7763157, "SRX21396039", "SRS18636197", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0021, 0.0, 0.00026, 0.0, 0.99859, 1.0, 0.71022, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25190, "SRR25670737", "SRX21396038", "SRS18636196", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 128cell PAL seq v4", "GSM7716867", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 128cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716867", "GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER", "GSM7716867 r1", "GSM7716867", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2104868443.0, 6856249.0, "GSM7716867 r1", "0:52 1:255", "A:539122676;C:505234642;G:558793048;T:495876292;N:5841785", 52, 255, null, null, 539122676, 505234642, 558793048, 495876292, 5841785, "SRX21396038", "SRS18636196", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00035, 0.29379, 7e-05, 0.01129, 0.99949, 0.99971, 0.55882, 0.79591, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25191, "SRR25670738", "SRX21396038", "SRS18636196", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 128cell PAL seq v4", "GSM7716867", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 128cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716867", "GSM7716867: Fish embryo mRNA 128cell PAL seq v4; Danio rerio; OTHER", "GSM7716867 r1", "GSM7716867", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_128cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3135806371.0, 10214353.0, "GSM7716867 r2", "0:52 1:255", "A:776612486;C:774126305;G:853951502;T:724788612;N:6327466", 52, 255, null, null, 776612486, 774126305, 853951502, 724788612, 6327466, "SRX21396038", "SRS18636196", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00066, 0.0, 0.00011, 0.0, 0.99939, 1.0, 0.55737, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25192, "SRR25670739", "SRX21396037", "SRS18636195", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 8cell PAL seq v4", "GSM7716866", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 8cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716866", "GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER", "GSM7716866 r1", "GSM7716866", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2618998887.0, 8530941.0, "GSM7716866 r1", "0:52 1:255", "A:673066508;C:641446717;G:706546263;T:590452494;N:7486905", 52, 255, null, null, 673066508, 641446717, 706546263, 590452494, 7486905, "SRX21396037", "SRS18636195", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.0009, 0.43244, 0.00014, 0.0054, 0.99902, 0.99967, 0.54901, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25193, "SRR25670740", "SRX21396037", "SRS18636195", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 8cell PAL seq v4", "GSM7716866", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 8cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716866", "GSM7716866: Fish embryo mRNA 8cell PAL seq v4; Danio rerio; OTHER", "GSM7716866 r1", "GSM7716866", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_8cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3028839589.0, 9865927.0, "GSM7716866 r2", "0:52 1:255", "A:756368817;C:758868409;G:836949742;T:670545278;N:6107343", 52, 255, null, null, 756368817, 758868409, 836949742, 670545278, 6107343, "SRX21396037", "SRS18636195", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00156, 0.0, 0.00026, 0.0, 0.99835, 1.0, 0.44791, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25194, "SRR25670741", "SRX21396036", "SRS18636194", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 1cell PAL seq v4", "GSM7716865", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716865", "GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER", "GSM7716865 r1", "GSM7716865", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep1_raw_read2.fastq.gz", "fastq fastq", 2050143851.0, 6677993.0, "GSM7716865 r1", "0:52 1:255", "A:536391564;C:527126186;G:557802929;T:422990166;N:5833006", 52, 255, null, null, 536391564, 527126186, 557802929, 422990166, 5833006, "SRX21396036", "SRS18636194", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00016, 0.46479, 4e-05, 0.01408, 0.99979, 0.99969, 0.54545, 1.0, 52, 255, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [25195, "SRR25670742", "SRX21396036", "SRS18636194", "SRP455680", "PRJNA1006406", "Control of polyA tail length and translation in vertebrate oocytes and early embryos", "GSE241107", "Other", "During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.", null, null, null, "Fish embryo mRNA 1cell PAL seq v4", "GSM7716865", null, "source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing", "Fish embryo mRNA 1cell PAL seq v4", "For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters \u201c m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7\u201d. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters \u201c  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate\u201d. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4\u20137 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4", "embryo", null, "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer\u2019s suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "tissue:embryo|treatment:N1", "GSM7716865", "GSM7716865: Fish embryo mRNA 1cell PAL seq v4; Danio rerio; OTHER", "GSM7716865 r1", "GSM7716865", "1", "Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 \u00b5g/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase\u2022In in a volume of 10 \u00b5l per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4\u00b0C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37\u00b0C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3\u02b9 adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 \u00b5l. The RNA and oligos were annealed by incubation at 70\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 40 \u00b5l MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 \u00b5l 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 \u00b5l 2x SSC. The RNA was eluted from the beads first with 100 \u00b5l 10 mM HEPES pH 7.5 at 65\u00b0C for 3 min and then second with 100 \u00b5l water at 65\u00b0C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 \u00b5l water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3\u02b9 adapter in a 10 \u00b5l reaction containing 5 \u00b5M 3\u02b9 adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/\u00b5l T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23\u00b0C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 \u00b5l water. The ligated RNA was mixed with 0.6 \u00b5l 100 \u00b5M reverse transcription primer KXS037 in a total volume of 12 \u00b5l  incubated at 65\u00b0C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 \u00b5l reaction containing 1x First Strand Buffer  500 \u00b5M dNTPs  5 mM dithiothreitol  1 unit/\u00b5l SUPERase\u2022In  and 200 units SuperScript III Thermo Fisher  18080044 at 50\u00b0C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 \u00b5l 1 M NaOH at 90\u00b0C for 10 min  followed by neutralization with 36.7 \u00b5l 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 \u00b5l PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10\u201315 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3\u02b9 adapter KXS013 was used for 3\u02b9 end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 \u00b5l. The cDNAs and the oligo were annealed by incubation at 65\u00b0C for 5 min and then slowly cooling to 23\u00b0C at 0.1\u00b0C/sec. The annealed mixture was combined with 100 \u00b5l MyOne Streptavidin C1 beads and incubated for 20 min at 23\u00b0C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 \u00b5l 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 \u00b5l water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP455680", null, null, "Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_1cell_PAL_seq_v4_rep2_raw_read2.fastq.gz", "fastq fastq", 3406093776.0, 11094768.0, "GSM7716865 r2", "0:52 1:255", "A:868054279;C:890446070;G:945289336;T:695324057;N:6980034", 52, 255, null, null, 868054279, 890446070, 945289336, 695324057, 6980034, "SRX21396036", "SRS18636194", "SRA1694849", "Whitehead Institute", "Whitehead Institute", 2, 0.00049, 0.0, 0.00014, 0.0, 0.99939, 1.0, 0.58974, null, 52, 255, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2023-08-17", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28725, "SRR26623262", "SRX22323921", "SRS19374450", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep1  cirbpb scars", "GSM7875190", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep1  cirbpb scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875190", "GSM7875190: Lineage tracing rep1  cirbpb scars; Danio rerio; OTHER", "GSM7875190 r1", "GSM7875190", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz", "fastq fastq", 157576336.0, 949552.0, "GSM7875190 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323921", "SRS19374450", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00141, 0.78069, 0.00053, 0.00877, 0.99857, 0.97822, 0.33536, 0.05199, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28726, "SRR26623263", "SRX22323920", "SRS19374449", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep1  cfl1 scars", "GSM7875189", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep1  cfl1 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875189", "GSM7875189: Lineage tracing rep1  cfl1 scars; Danio rerio; OTHER", "GSM7875189 r1", "GSM7875189", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz", "fastq fastq", 381453696.0, 2184402.0, "GSM7875189 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323920", "SRS19374449", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.0002, 0.91626, 0.00014, 0.00132, 0.99987, 0.99726, 0.16666, 0.56363, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28727, "SRR26623264", "SRX22323919", "SRS19374448", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep1  actb2 scars", "GSM7875188", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep1  actb2 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875188", "GSM7875188: Lineage tracing rep1  actb2 scars; Danio rerio; OTHER", "GSM7875188 r1", "GSM7875188", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz", "fastq fastq", 491682118.0, 2851156.0, "GSM7875188 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323919", "SRS19374448", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00051, 0.41901, 0.00032, 0.0029, 0.99945, 0.99182, 0.57575, 0.007, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28728, "SRR26623265", "SRX22323918", "SRS19374446", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep1  actb1 scars", "GSM7875187", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep1  actb1 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875187", "GSM7875187: Lineage tracing rep1  actb1 scars; Danio rerio; OTHER", "GSM7875187 r1", "GSM7875187", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz", "fastq fastq", 390405832.0, 2283319.0, "GSM7875187 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323918", "SRS19374446", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00038, 0.73548, 0.00017, 0.00057, 0.99963, 0.99571, 0.29729, 0.00243, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28729, "SRR26623266", "SRX22323917", "SRS19374447", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Brain 23   telencephalon  Notch inhibition  scSLAMseq", "GSM7875186", null, "source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT|geo loc name:missing|collection date:missing", "Brain 23   telencephalon  Notch inhibition  scSLAMseq", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq", "adult brain", "Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 \u00b5M DAPT Gamma Secretase Inhibitor  Sigma Aldrich for 48 hours.", "The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 \u00b5l 100 mM IAA to 800 \u00b5l fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 \u00b5m filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT", "GSM7875186", "GSM7875186: Brain 23   telencephalon  Notch inhibition  scSLAMseq; Danio rerio; OTHER", "GSM7875186 r1", "GSM7875186", "1", "The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 \u00b5l 100 mM IAA to 800 \u00b5l fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 \u00b5m filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "b23_ni_tre_R1.fastq.gz b23_ni_tre_R2.fastq.gz", "fastq fastq", 62392458570.0, 271271559.0, "GSM7875186 r1", "0:28 1:202", "A:18682905645;C:13783082970;G:14751373116;T:15161083446;N:14013393", 28, 202, null, null, 18682905645, 13783082970, 14751373116, 15161083446, 14013393, "SRX22323917", "SRS19374447", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.01404, 0.82351, 0.00466, 0.1026, 0.99129, 0.86774, 0.36033, 0.67345, 28, 202, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28730, "SRR26623267", "SRX22323916", "SRS19374445", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Brain 22   telencephalon  control  scSLAMseq", "GSM7875185", null, "source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO|geo loc name:missing|collection date:missing", "Brain 22   telencephalon  control  scSLAMseq", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq", "adult brain", "Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours.", "The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 \u00b5l 100 mM IAA to 800 \u00b5l fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 \u00b5m filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO", "GSM7875185", "GSM7875185: Brain 22   telencephalon  control  scSLAMseq; Danio rerio; OTHER", "GSM7875185 r1", "GSM7875185", "1", "The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 \u00b5l 100 mM IAA to 800 \u00b5l fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 \u00b5m filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "b22_ni_con_R1.fastq.gz b22_ni_con_R2.fastq.gz", "fastq fastq", 59793114490.0, 259970063.0, "GSM7875185 r1", "0:28 1:202", "A:18600519530;C:12714987967;G:14147370465;T:14316863915;N:13372613", 28, 202, null, null, 18600519530, 12714987967, 14147370465, 14316863915, 13372613, "SRX22323916", "SRS19374445", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.01402, 0.79448, 0.00498, 0.11405, 0.99074, 0.8518, 0.39874, 0.67082, 28, 202, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28754, "SRR26623291", "SRX22323897", "SRS19374426", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep2  ube2e1 scars", "GSM7875196", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep2  ube2e1 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875196", "GSM7875196: Lineage tracing rep2  ube2e1 scars; Danio rerio; OTHER", "GSM7875196 r1", "GSM7875196", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz", "fastq fastq", 213092161.0, 1190459.0, "GSM7875196 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323897", "SRS19374426", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00752, 0.90776, 0.00286, 0.01739, 0.99346, 0.95444, 0.46002, 0.96817, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28755, "SRR26623292", "SRX22323896", "SRS19374425", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep2  rpl39 scars", "GSM7875195", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep2  rpl39 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875195", "GSM7875195: Lineage tracing rep2  rpl39 scars; Danio rerio; OTHER", "GSM7875195 r1", "GSM7875195", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz", "fastq fastq", 1023403502.0, 5717338.0, "GSM7875195 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323896", "SRS19374425", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00086, 0.83744, 0.0003, 0.00337, 0.99845, 0.97057, 0.26605, 0.40241, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28756, "SRR26623293", "SRX22323895", "SRS19374424", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep2  cirbpb scars", "GSM7875194", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep2  cirbpb scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875194", "GSM7875194: Lineage tracing rep2  cirbpb scars; Danio rerio; OTHER", "GSM7875194 r1", "GSM7875194", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz", "fastq fastq", 276120388.0, 1542572.0, "GSM7875194 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323895", "SRS19374424", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00206, 0.80328, 0.00078, 0.00662, 0.9975, 0.98039, 0.55421, 0.0258, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28757, "SRR26623294", "SRX22323894", "SRS19374423", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep2  cfl1 scars", "GSM7875193", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep2  cfl1 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875193", "GSM7875193: Lineage tracing rep2  cfl1 scars; Danio rerio; OTHER", "GSM7875193 r1", "GSM7875193", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz", "fastq fastq", 791318009.0, 4420771.0, "GSM7875193 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323894", "SRS19374423", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00067, 0.46079, 0.00055, 0.16353, 0.99965, 0.99332, 0.52631, 0.44939, 28, 151, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28758, "SRR26623295", "SRX22323893", "SRS19374421", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep1  ube2e1 scars", "GSM7875192", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep1  ube2e1 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875192", "GSM7875192: Lineage tracing rep1  ube2e1 scars; Danio rerio; OTHER", "GSM7875192 r1", "GSM7875192", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz", "fastq fastq", 99407618.0, 601781.0, "GSM7875192 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323893", "SRS19374421", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00657, 0.84532, 0.00205, 0.03049, 0.99537, 0.95286, 0.43306, 0.19203, 28, 150, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [28759, "SRR26623296", "SRX22323892", "SRS19374422", "SRP469552", "PRJNA1034159", "Dissecting the spatiotemporal diversity of adult neural stem cells", "GSE246714", "Other", "Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.", null, "pubmed:38365956", null, "Lineage tracing rep1  rpl39 scars", "GSM7875191", null, "source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing", "Lineage tracing rep1  rpl39 scars", "The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.", "adult brain", null, "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]", "GSM7875191", "GSM7875191: Lineage tracing rep1  rpl39 scars; Danio rerio; OTHER", "GSM7875191 r1", "GSM7875191", "1", "Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz", "fastq fastq", 401898718.0, 2276836.0, "GSM7875191 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323892", "SRS19374422", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", 2, 0.00037, 0.2642, 0.00015, 0.00086, 0.99922, 0.99026, 0.23076, 0.42455, 28, 120, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [29210, "SRR27489726", "SRX23160983", "SRS20111140", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 6hpf replica A", "MPRA repA fractions 4 5 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:10|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 6hpf replica A", "Library 10", "Library 10", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13762167482.0, 45570091.0, "BSSE QGF 206645 HGWLYDSX3 3 MPRA repA fractions 4 5 6hpf CTCTCGTC TATAACCT S10 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3449173111;C:3620318973;G:3412595233;T:3279391764;N:688401", 151, 151, null, null, 3449173111, 3620318973, 3412595233, 3279391764, 688401, "SRX23160983", "SRS20111140", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01348, 9e-05, 0.00033, 1e-05, 0.99151, 0.99973, 0.41104, 0.57142, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29211, "SRR27489727", "SRX23160982", "SRS20111139", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 6hpf replica A", "MPRA repA input 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:9|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 6hpf replica A", "Library 9", "Library 9", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 13570263998.0, 44934649.0, "BSSE QGF 206644 HGWLYDSX3 3 MPRA repA input 6hpf TCTCTACT CGCGGTTC S9 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3444180060;C:3577051220;G:3264051077;T:3284343514;N:638127", 151, 151, null, null, 3444180060, 3577051220, 3264051077, 3284343514, 638127, "SRX23160982", "SRS20111139", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01809, 5e-05, 0.00042, 0.0, 0.99013, 0.99985, 0.41794, 0.57142, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29212, "SRR27489728", "SRX23160981", "SRS20111138", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 4hpf replica A", "MPRA repA fractions 8 9 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:8|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 4hpf replica A", "Library 8", "Library 8", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12066108000.0, 39954000.0, "BSSE QGF 206643 HGWLYDSX3 3 MPRA repA fractions 8 9 4hpf GACCTGAA TTGGTGAG S8 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3060316371;C:3136678983;G:2965588104;T:2902920606;N:603936", 151, 151, null, null, 3060316371, 3136678983, 2965588104, 2902920606, 603936, "SRX23160981", "SRS20111138", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01336, 5e-05, 0.00027, 0.0, 0.99143, 0.99983, 0.40418, 0.125, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29213, "SRR27489729", "SRX23160980", "SRS20111142", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 4hpf replica A", "MPRA repA fractions 6 7 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:7|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 4hpf replica A", "Library 7", "Library 7", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 11998643314.0, 39730607.0, "BSSE QGF 206642 HGWLYDSX3 3 MPRA repA fractions 6 7 4hpf AGTTCAGG CCAACAGA S7 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3044270548;C:3145201016;G:2907229129;T:2901344613;N:598008", 151, 151, null, null, 3044270548, 3145201016, 2907229129, 2901344613, 598008, "SRX23160980", "SRS20111142", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01631, 0.00013, 0.00035, 1e-05, 0.99101, 0.99965, 0.40542, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29214, "SRR27489730", "SRX23160979", "SRS20111137", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 4hpf replica A", "MPRA repA fractions 4 5 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:6|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 4hpf replica A", "Library 6", "Library 6", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12838157410.0, 42510455.0, "BSSE QGF 206641 HGWLYDSX3 3 MPRA repA fractions 4 5 4hpf TGGATCGA GTGCGATA S6 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3238698530;C:3377705608;G:3143460419;T:3077655243;N:637610", 151, 151, null, null, 3238698530, 3377705608, 3143460419, 3077655243, 637610, "SRX23160979", "SRS20111137", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01549, 3e-05, 0.00042, 1e-05, 0.99097, 0.99995, 0.42138, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29215, "SRR27489731", "SRX23160978", "SRS20111136", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "RNA product", "control RNA library", "RNA mMessage MPRA library", null, "strain:not applicable|age:not applicable|dev stage:not applicable|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:not applicable|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:not applicable|growth protocol:not applicable|sample type:IVT mRNA|sample number:50|replicate:unique sample|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "control RNA library", "Library 50", "Library 50", "PCR product was amplified from DNA plasmid pool with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16695252486.0, 55282293.0, "BSSE QGF 206685 HGWLYDSX3 3 RNA mMessage MPRA library test GGTTATAA GATATCGA S50 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4275447149;C:4413405571;G:3936523108;T:4069049357;N:827301", 151, 151, null, null, 4275447149, 4413405571, 3936523108, 4069049357, 827301, "SRX23160978", "SRS20111136", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02176, 0.00021, 0.00058, 2e-05, 0.99056, 0.99933, 0.41475, 0.48571, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29216, "SRR27489733", "SRX23160976", "SRS20111134", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 10hpf replica C", "MPRA repC fractions 8 9 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:48|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 10hpf replica C", "Library 48", "Library 48", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16074911568.0, 53228184.0, "BSSE QGF 206683 HGWLYDSX3 3 MPRA repC fractions 8 9 10hpf CAACAATG CTTCACGG S48 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4029048727;C:4167204709;G:4036912991;T:3840941866;N:803275", 151, 151, null, null, 4029048727, 4167204709, 4036912991, 3840941866, 803275, "SRX23160976", "SRS20111134", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.00795, 0.00021, 0.00019, 2e-05, 0.99263, 0.99935, 0.45247, 0.62857, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29217, "SRR27489734", "SRX23160975", "SRS20111132", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 10hpf replica C", "MPRA repC fractions 6 7 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:47|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 10hpf replica C", "Library 47", "Library 47", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16211925948.0, 53681874.0, "BSSE QGF 206682 HGWLYDSX3 3 MPRA repC fractions 6 7 10hpf GGTGAACC GCGTTGGA S47 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4078470905;C:4239434649;G:4000426230;T:3892801664;N:792500", 151, 151, null, null, 4078470905, 4239434649, 4000426230, 3892801664, 792500, "SRX23160975", "SRS20111132", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01232, 0.00028, 0.00027, 5e-05, 0.99166, 0.99926, 0.4522, 0.61904, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29218, "SRR27489735", "SRX23160974", "SRS20111131", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 10hpf replica C", "MPRA repC fractions 4 5 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:46|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 10hpf replica C", "Library 46", "Library 46", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 18761117310.0, 62122905.0, "BSSE QGF 206681 HGWLYDSX3 3 MPRA repC fractions 4 5 10hpf AACAGGTT ATACCAAG S46 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4746221682;C:4940258209;G:4549993563;T:4523714877;N:928979", 151, 151, null, null, 4746221682, 4940258209, 4549993563, 4523714877, 928979, "SRX23160974", "SRS20111131", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01785, 0.0002, 0.00043, 3e-05, 0.9908, 0.99951, 0.45866, 0.6, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29219, "SRR27489736", "SRX23160973", "SRS20111130", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 10hpf replica C", "MPRA repC input 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:45|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 10hpf replica C", "Library 45", "Library 45", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15148053334.0, 50159117.0, "BSSE QGF 206680 HGWLYDSX3 3 MPRA repC input 10hpf GCGCTCTA GCTCCGAC S45 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3877492548;C:4007711111;G:3560735163;T:3701356537;N:757975", 151, 151, null, null, 3877492548, 4007711111, 3560735163, 3701356537, 757975, "SRX23160973", "SRS20111130", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02196, 3e-05, 0.00062, 1e-05, 0.98944, 0.99993, 0.4404, 0.66666, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29220, "SRR27489737", "SRX23160972", "SRS20111129", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 6hpf replica C", "MPRA repC fractions 8 9 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:44|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 6hpf replica C", "Library 44", "Library 44", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 14506315716.0, 48034158.0, "BSSE QGF 206679 HGWLYDSX3 3 MPRA repC fractions 8 9 6hpf ATATCTCG ATCTTAGT S44 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3655344763;C:3770081597;G:3599601074;T:3480562617;N:725665", 151, 151, null, null, 3655344763, 3770081597, 3599601074, 3480562617, 725665, "SRX23160972", "SRS20111129", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01152, 0.00012, 0.00021, 1e-05, 0.99204, 0.99963, 0.40859, 0.47368, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29221, "SRR27489738", "SRX23160971", "SRS20111128", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 6hpf replica C", "MPRA repC fractions 6 7 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:43|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 6hpf replica C", "Library 43", "Library 43", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 14912162946.0, 49378023.0, "BSSE QGF 206678 HGWLYDSX3 3 MPRA repC fractions 6 7 6hpf ACCTTGGC GGCCTCAT S43 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3752402181;C:3897191999;G:3682100517;T:3579734634;N:733615", 151, 151, null, null, 3752402181, 3897191999, 3682100517, 3579734634, 733615, "SRX23160971", "SRS20111128", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01301, 0.0001, 0.00023, 0.0, 0.99131, 0.99963, 0.41128, 0.44444, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29222, "SRR27489739", "SRX23160970", "SRS20111127", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 6hpf replica C", "MPRA repC fractions 4 5 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:42|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 6hpf replica C", "Library 42", "Library 42", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16464627468.0, 54518634.0, "BSSE QGF 206677 HGWLYDSX3 3 MPRA repC fractions 4 5 6hpf GTTCCAAT AATTCTGC S42 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4169088631;C:4342123158;G:3994621055;T:3957976348;N:818276", 151, 151, null, null, 4169088631, 4342123158, 3994621055, 3957976348, 818276, "SRX23160970", "SRS20111127", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01689, 8e-05, 0.00051, 0.0, 0.99107, 0.99973, 0.40071, 0.53846, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29223, "SRR27489740", "SRX23160969", "SRS20111125", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 6hpf replica C", "MPRA repC input 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:41|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 6hpf replica C", "Library 41", "Library 41", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 10859083158.0, 35957229.0, "BSSE QGF 206676 HGWLYDSX3 3 MPRA repC input 6hpf GCAATGCA GGAACGTT S41 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2762807814;C:2857106152;G:2613305234;T:2625327901;N:536057", 151, 151, null, null, 2762807814, 2857106152, 2613305234, 2625327901, 536057, "SRX23160969", "SRS20111125", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01753, 0.0, 0.00047, 0.0, 0.9907, 1.0, 0.40097, null, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29224, "SRR27489741", "SRX23160968", "SRS20111133", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 4hpf replica A", "MPRA repA input 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:5|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 4hpf replica A", "Library 5", "Library 5", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13631534966.0, 45137533.0, "BSSE QGF 206640 HGWLYDSX3 3 MPRA repA input 4hpf CAAGCTAG ACATAGCG S5 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3486253250;C:3611078376;G:3219396920;T:3314128840;N:677580", 151, 151, null, null, 3486253250, 3611078376, 3219396920, 3314128840, 677580, "SRX23160968", "SRS20111133", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02225, 2e-05, 0.00066, 0.0, 0.98975, 0.99993, 0.40257, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29225, "SRR27489742", "SRX23160967", "SRS20111126", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 4hpf replica C", "MPRA repC fractions 8 9 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:40|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 4hpf replica C", "Library 40", "Library 40", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16854209582.0, 55808641.0, "BSSE QGF 206675 HGWLYDSX3 3 MPRA repC fractions 8 9 4hpf ATGGCATG AAGGTACC S40 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4270727222;C:4383022813;G:4143081915;T:4056541855;N:835777", 151, 151, null, null, 4270727222, 4383022813, 4143081915, 4056541855, 835777, "SRX23160967", "SRS20111126", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01329, 0.00015, 0.00029, 2e-05, 0.99141, 0.99953, 0.4263, 0.47826, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29226, "SRR27489743", "SRX23160966", "SRS20111124", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 4hpf replica C", "MPRA repC fractions 6 7 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:39|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 4hpf replica C", "Library 39", "Library 39", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12146174844.0, 40219122.0, "BSSE QGF 206674 HGWLYDSX3 3 MPRA repC fractions 6 7 4hpf GGAGCGTC GTCCGTGC S39 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3060215849;C:3176615755;G:3002666854;T:2906066243;N:610143", 151, 151, null, null, 3060215849, 3176615755, 3002666854, 2906066243, 610143, "SRX23160966", "SRS20111124", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01309, 0.0002, 0.00031, 0.0, 0.99164, 0.99939, 0.40018, 0.57142, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29227, "SRR27489744", "SRX23160965", "SRS20111123", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 4hpf replica C", "MPRA repC fractions 4 5 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:38|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 4hpf replica C", "Library 38", "Library 38", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 14100203330.0, 46689415.0, "BSSE QGF 206673 HGWLYDSX3 3 MPRA repC fractions 4 5 4hpf AAGATACT ACTTACAT S38 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3544539088;C:3702795841;G:3493240125;T:3358929671;N:698605", 151, 151, null, null, 3544539088, 3702795841, 3493240125, 3358929671, 698605, "SRX23160965", "SRS20111123", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01368, 0.00016, 0.00037, 0.0, 0.99107, 0.99951, 0.40864, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29228, "SRR27489745", "SRX23160964", "SRS20111120", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 4hpf replica C", "MPRA repC input 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:37|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 4hpf replica C", "Library 37", "Library 37", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 10925301792.0, 36176496.0, "BSSE QGF 206672 HGWLYDSX3 3 MPRA repC input 4hpf GCGCAAGC TCACGCCG S37 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2802490901;C:2878602103;G:2592316062;T:2651349641;N:543085", 151, 151, null, null, 2802490901, 2878602103, 2592316062, 2651349641, 543085, "SRX23160964", "SRS20111120", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02108, 3e-05, 0.0006, 0.0, 0.98981, 0.99991, 0.42181, 0.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29229, "SRR27489746", "SRX23160963", "SRS20111121", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica C", "MPRA repC fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica C", "Library 36", "Library 36", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13085558528.0, 43329664.0, "BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985", 151, 151, null, null, 3305413622, 3391845548, 3249932870, 3137708503, 657985, "SRX23160963", "SRS20111121", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01098, 8e-05, 0.00025, 0.0, 0.99216, 0.99973, 0.4317, 0.61538, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29230, "SRR27489747", "SRX23160962", "SRS20111119", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica C", "MPRA repC fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica C", "Library 35", "Library 35", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16647721914.0, 55124907.0, "BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108", 151, 151, null, null, 4231542934, 4348688006, 4050131444, 4016534422, 825108, "SRX23160962", "SRS20111119", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01514, 0.00017, 0.00035, 3e-05, 0.99109, 0.99955, 0.4372, 0.30434, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29231, "SRR27489748", "SRX23160961", "SRS20111118", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica C", "MPRA repC fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica C", "Library 34", "Library 34", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15431181052.0, 51096626.0, "BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999", 151, 151, null, null, 3856018869, 4036338306, 3877988553, 3660059325, 775999, "SRX23160961", "SRS20111118", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01114, 8e-05, 0.00028, 0.0, 0.99192, 0.99975, 0.42956, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29232, "SRR27489749", "SRX23160960", "SRS20111117", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica C", "MPRA repC input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica C", "Library 33", "Library 33", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 11771229160.0, 38977580.0, "BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080", 151, 151, null, null, 2999574420, 3115525474, 2806539264, 2849003922, 586080, "SRX23160960", "SRS20111117", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01997, 2e-05, 0.00054, 0.0, 0.99022, 0.99993, 0.41853, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29233, "SRR27489750", "SRX23160959", "SRS20111116", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 10hpf replica B", "MPRA repB fractions 8 9 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:32|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 10hpf replica B", "Library 32", "Library 32", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12683073766.0, 41996933.0, "BSSE QGF 206667 HGWLYDSX3 3 MPRA repB fractions 8 9 10hpf TCGTAGTG AGACTTGG S32 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3165850297;C:3286094227;G:3205853472;T:3024640146;N:635624", 151, 151, null, null, 3165850297, 3286094227, 3205853472, 3024640146, 635624, "SRX23160959", "SRS20111116", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.00973, 0.00093, 0.00036, 0.00015, 0.99265, 0.99819, 0.4701, 0.61111, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29234, "SRR27489751", "SRX23160958", "SRS20111115", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 10hpf replica B", "MPRA repB fractions 6 7 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:31|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 10hpf replica B", "Library 31", "Library 31", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11187950286.0, 37046193.0, "BSSE QGF 206666 HGWLYDSX3 3 MPRA repB fractions 6 7 10hpf GATTCTGC GACGAGAG S31 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2805602272;C:2927866458;G:2773076846;T:2680845208;N:559502", 151, 151, null, null, 2805602272, 2927866458, 2773076846, 2680845208, 559502, "SRX23160958", "SRS20111115", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01142, 0.0002, 0.00018, 2e-05, 0.99243, 0.99943, 0.45894, 0.54838, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29235, "SRR27489752", "SRX23160957", "SRS20111114", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica A", "MPRA repA fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica A", "Library 4", "Library 4", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12108626278.0, 40094789.0, "BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268", 151, 151, null, null, 3079403604, 3149095123, 2953175005, 2926352278, 600268, "SRX23160957", "SRS20111114", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.014, 5e-05, 0.00032, 0.0, 0.99137, 0.99987, 0.45127, 0.28571, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29236, "SRR27489753", "SRX23160956", "SRS20111113", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 10hpf replica B", "MPRA repB fractions 4 5 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:30|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 10hpf replica B", "Library 30", "Library 30", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15465851256.0, 51211428.0, "BSSE QGF 206665 HGWLYDSX3 3 MPRA repB fractions 4 5 10hpf AGCCTCAT AGTAGAGA S30 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3889753740;C:4075740540;G:3791174754;T:3708409198;N:773024", 151, 151, null, null, 3889753740, 4075740540, 3791174754, 3708409198, 773024, "SRX23160956", "SRS20111113", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01609, 0.00014, 0.0003, 3e-05, 0.99139, 0.99959, 0.4335, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29237, "SRR27489754", "SRX23160955", "SRS20111112", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 10hpf replica B", "MPRA repB input 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:29|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 10hpf replica B", "Library 29", "Library 29", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12592035866.0, 41695483.0, "BSSE QGF 206664 HGWLYDSX3 3 MPRA repB input 10hpf CGTTAGAA TTCAGGTC S29 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3220865280;C:3326103488;G:2978281202;T:3066156448;N:629448", 151, 151, null, null, 3220865280, 3326103488, 2978281202, 3066156448, 629448, "SRX23160955", "SRS20111112", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02168, 1e-05, 0.0006, 0.0, 0.98993, 0.99997, 0.41273, 1.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29238, "SRR27489755", "SRX23160954", "SRS20111122", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 6hpf replica B", "MPRA repB fractions 8 9 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:28|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 6hpf replica B", "Library 28", "Library 28", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12606651156.0, 41743878.0, "BSSE QGF 206663 HGWLYDSX3 3 MPRA repB fractions 8 9 6hpf TACCGAGG CCTGAACT S28 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3184687427;C:3283680489;G:3107570485;T:3030085619;N:627136", 151, 151, null, null, 3184687427, 3283680489, 3107570485, 3030085619, 627136, "SRX23160954", "SRS20111122", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01219, 7e-05, 0.00028, 0.0, 0.99182, 0.99977, 0.42217, 0.45454, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29239, "SRR27489756", "SRX23160953", "SRS20111110", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 6hpf replica B", "MPRA repB fractions 6 7 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:27|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 6hpf replica B", "Library 27", "Library 27", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 13738263880.0, 45490940.0, "BSSE QGF 206662 HGWLYDSX3 3 MPRA repB fractions 6 7 6hpf AATGCCTC TCGATCCA S27 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3463772316;C:3608023656;G:3363805269;T:3301974573;N:688066", 151, 151, null, null, 3463772316, 3608023656, 3363805269, 3301974573, 688066, "SRX23160953", "SRS20111110", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01443, 0.00014, 0.00028, 1e-05, 0.99117, 0.99957, 0.38916, 0.45833, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29240, "SRR27489757", "SRX23160952", "SRS20111111", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 6hpf replica B", "MPRA repB fractions 4 5 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:26|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 6hpf replica B", "Library 26", "Library 26", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 10624262152.0, 35179676.0, "BSSE QGF 206661 HGWLYDSX3 3 MPRA repB fractions 4 5 6hpf GGCATTCT CTAGCTTG S26 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2680084455;C:2804915710;G:2592024460;T:2546707250;N:530277", 151, 151, null, null, 2680084455, 2804915710, 2592024460, 2546707250, 530277, "SRX23160952", "SRS20111111", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01636, 0.00013, 0.00046, 0.0, 0.99088, 0.99959, 0.39222, 0.40909, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29241, "SRR27489758", "SRX23160951", "SRS20111109", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 6hpf replica B", "MPRA repB input 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:25|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 6hpf replica B", "Library 25", "Library 25", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 10153888998.0, 33622149.0, "BSSE QGF 206660 HGWLYDSX3 3 MPRA repB input 6hpf TTACAGGA TGACAAGC S25 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2587160061;C:2673241688;G:2432503358;T:2460478928;N:504963", 151, 151, null, null, 2587160061, 2673241688, 2432503358, 2460478928, 504963, "SRX23160951", "SRS20111109", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01911, 2e-05, 0.00061, 0.0, 0.99064, 0.99995, 0.42802, 0.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29242, "SRR27489759", "SRX23160950", "SRS20111107", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 4hpf replica B", "MPRA repB fractions 8 9 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:24|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 4hpf replica B", "Library 24", "Library 24", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11600767978.0, 38413139.0, "BSSE QGF 206659 HGWLYDSX3 3 MPRA repB fractions 8 9 4hpf CCGTGAAG CAGTGGAT S24 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2943303855;C:3024500200;G:2833306086;T:2799077405;N:580432", 151, 151, null, null, 2943303855, 3024500200, 2833306086, 2799077405, 580432, "SRX23160950", "SRS20111107", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01371, 0.00013, 0.00031, 1e-05, 0.99143, 0.99955, 0.41912, 0.5909, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29243, "SRR27489760", "SRX23160949", "SRS20111106", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 4hpf replica B", "MPRA repB fractions 6 7 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:23|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 4hpf replica B", "Library 23", "Library 23", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13216553444.0, 43763422.0, "BSSE QGF 206658 HGWLYDSX3 3 MPRA repB fractions 6 7 4hpf CTTGGTAT CCAAGTCC S23 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3339016083;C:3457419680;G:3233764657;T:3185687490;N:665534", 151, 151, null, null, 3339016083, 3457419680, 3233764657, 3185687490, 665534, "SRX23160949", "SRS20111106", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01431, 0.00024, 0.00034, 1e-05, 0.99135, 0.99924, 0.41915, 0.45238, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29244, "SRR27489761", "SRX23160948", "SRS20111105", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 4hpf replica B", "MPRA repB fractions 4 5 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:22|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 4hpf replica B", "Library 22", "Library 22", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11938250562.0, 39530631.0, "BSSE QGF 206657 HGWLYDSX3 3 MPRA repB fractions 4 5 4hpf ATGAGGCC GTTAATTG S22 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3040684418;C:3144238599;G:2873359599;T:2879374531;N:593415", 151, 151, null, null, 3040684418, 3144238599, 2873359599, 2879374531, 593415, "SRX23160948", "SRS20111105", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.0185, 8e-05, 0.00056, 0.0, 0.9903, 0.99969, 0.4376, 0.4, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29245, "SRR27489762", "SRX23160947", "SRS20111104", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 4hpf replica B", "MPRA repB input 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:21|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 4hpf replica B", "Library 21", "Library 21", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 14482326346.0, 47954723.0, "BSSE QGF 206656 HGWLYDSX3 3 MPRA repB input 4hpf GCAGAATT ACCGGCCA S21 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3697691325;C:3838972714;G:3432418300;T:3512522230;N:721777", 151, 151, null, null, 3697691325, 3838972714, 3432418300, 3512522230, 721777, "SRX23160947", "SRS20111104", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.0211, 2e-05, 0.00055, 0.0, 0.9903, 0.99993, 0.42543, 0.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29246, "SRR27489763", "SRX23160946", "SRS20111108", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica A", "MPRA repA fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica A", "Library 3", "Library 3", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12524202136.0, 41470868.0, "BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842", 151, 151, null, null, 3168466372, 3269998328, 3075956662, 3009160932, 619842, "SRX23160946", "SRS20111108", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01351, 7e-05, 0.00028, 0.0, 0.99168, 0.99977, 0.43472, 0.54545, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29247, "SRR27489764", "SRX23160945", "SRS20111103", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica B", "MPRA repB fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica B", "Library 20", "Library 20", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12514444214.0, 41438557.0, "BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303", 151, 151, null, null, 3174354240, 3246812350, 3082021359, 3010633962, 622303, "SRX23160945", "SRS20111103", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01121, 0.00016, 0.00027, 1e-05, 0.99204, 0.99953, 0.43533, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29248, "SRR27489765", "SRX23160944", "SRS20111102", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica B", "MPRA repB fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica B", "Library 19", "Library 19", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16535129670.0, 54752085.0, "BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421", 151, 151, null, null, 4184643114, 4312135767, 4051628900, 3985895468, 826421, "SRX23160944", "SRS20111102", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01416, 0.00017, 0.00031, 1e-05, 0.9917, 0.99941, 0.40732, 0.6, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29249, "SRR27489766", "SRX23160943", "SRS20111101", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica B", "MPRA repB fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica B", "Library 18", "Library 18", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12692870042.0, 42029371.0, "BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284", 151, 151, null, null, 3179006274, 3325152682, 3173386021, 3014687781, 637284, "SRX23160943", "SRS20111101", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01199, 8e-05, 0.0003, 1e-05, 0.99145, 0.99979, 0.40897, 0.36363, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29250, "SRR27489767", "SRX23160942", "SRS20111100", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica B", "MPRA repB input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica B", "Library 17", "Library 17", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13169436008.0, 43607404.0, "BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755", 151, 151, null, null, 3341908647, 3485072739, 3171200836, 3170595031, 658755, "SRX23160942", "SRS20111100", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01868, 5e-05, 0.0006, 0.0, 0.99038, 0.99983, 0.41955, 0.125, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29251, "SRR27489768", "SRX23160941", "SRS20111099", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 10hpf replica A", "MPRA repA fractions 8 9 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. 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