{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"smartseq\" and tissue_curation = \"Whole Organism\"", "rows": [[9775, "ERR3838754", "ERX3851420", "ERS4266444", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma prim5 wt rep2", "SAMEA6501995", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501995|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma prim5 wt rep2 p", "Soma prim5 wt rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "Somatic_prim5_rep2_R1.fastq.gz Somatic_prim5_rep2_R2.fastq.gz", "fastq fastq", 2664555542.0, 17942996.0, "E MTAB 8707:Somatic prim5 rep2 R", "0:74.25 1:74.25", "A:757990974;C:568005838;G:586848520;T:749991976;N:1718234", 74, 74, null, null, 757990974, 568005838, 586848520, 749991976, 1718234, "ERX3851420", "ERS4266444", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92034, 0.91779, 0.22669, 0.22761, 0.74769, 0.74911, 0.45866, 0.45282, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9776, "ERR3838753", "ERX3851419", "ERS4266443", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma prim5 wt rep1", "SAMEA6501994", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501994|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma prim5 wt rep1 p", "Soma prim5 wt rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "Somatic_prim5_rep1_R1.fastq.gz Somatic_prim5_rep1_R2.fastq.gz", "fastq fastq", 1847156504.0, 12386853.0, "E MTAB 8707:Somatic prim5 rep1 R", "0:74.56 1:74.56", "A:519724449;C:399975516;G:411702918;T:514818493;N:935128", 74, 74, null, null, 519724449, 399975516, 411702918, 514818493, 935128, "ERX3851419", "ERS4266443", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93526, 0.93319, 0.24244, 0.24304, 0.75073, 0.75201, 0.44773, 0.44885, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9777, "ERR3838752", "ERX3851418", "ERS4266442", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma prim5 Morpholino rep2", "SAMEA6501993", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501993|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma prim5 Morpholino rep2 p", "Soma prim5 Morpholino rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S14_R1.fastq.gz S14_R2.fastq.gz", "fastq fastq", 953947657.0, 6389852.0, "E MTAB 8707:S14 R", "0:74.64 1:74.65", "A:271485260;C:204208876;G:210319402;T:267490986;N:443133", 74, 74, null, null, 271485260, 204208876, 210319402, 267490986, 443133, "ERX3851418", "ERS4266442", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93577, 0.93619, 0.1141, 0.11516, 0.72644, 0.72892, 0.4694, 0.46965, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9778, "ERR3838751", "ERX3851417", "ERS4266441", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma prim5 Morpholino rep1", "SAMEA6501992", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501992|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma prim5 Morpholino rep1 p", "Soma prim5 Morpholino rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S12_R1.fastq.gz S12_R2.fastq.gz", "fastq fastq", 753719404.0, 5057589.0, "E MTAB 8707:S12 R", "0:74.51 1:74.52", "A:216097326;C:160004832;G:164724356;T:212507268;N:385622", 74, 74, null, null, 216097326, 160004832, 164724356, 212507268, 385622, "ERX3851417", "ERS4266441", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93958, 0.93943, 0.10854, 0.1092, 0.73267, 0.73663, 0.45629, 0.47862, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9779, "ERR3838750", "ERX3851416", "ERS4266440", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma prim5 5mismatch Morpholino rep2", "SAMEA6501991", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501991|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma prim5 5mismatch Morpholino rep2 p", "Soma prim5 5mismatch Morpholino rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S18_R1.fastq.gz S18_R2.fastq.gz", "fastq fastq", 847966718.0, 5668126.0, "E MTAB 8707:S18 R", "0:74.80 1:74.80", "A:230723434;C:191446710;G:197114792;T:228326953;N:354829", 74, 74, null, null, 230723434, 191446710, 197114792, 228326953, 354829, "ERX3851416", "ERS4266440", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92436, 0.92488, 0.08973, 0.09012, 0.73971, 0.74192, 0.45291, 0.45397, 76, 73, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9780, "ERR3838749", "ERX3851415", "ERS4266439", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma prim5 5mismatch Morpholino rep1", "SAMEA6501990", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501990|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma prim5 5mismatch Morpholino rep1 p", "Soma prim5 5mismatch Morpholino rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S16_R1.fastq.gz S16_R2.fastq.gz", "fastq fastq", 444518989.0, 2971315.0, "E MTAB 8707:S16 R", "0:74.80 1:74.80", "A:121398448;C:100282796;G:103112415;T:119559792;N:165538", 74, 74, null, null, 121398448, 100282796, 103112415, 119559792, 165538, "ERX3851415", "ERS4266439", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92469, 0.92438, 0.09917, 0.10006, 0.72279, 0.7251, 0.45852, 0.46016, 73, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9781, "ERR3838748", "ERX3851414", "ERS4266438", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma High rep2", "SAMEA6501989", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501989|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep2|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma High rep2 p", "Soma High rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "Fabio_High_rep2_soma_R1.fastq.gz Fabio_High_rep2_soma_R2.fastq.gz", "fastq fastq", 2072343523.0, 13904136.0, "E MTAB 8707:Fabio High rep2 soma R", "0:74.52 1:74.53", "A:596021076;C:439789413;G:451992691;T:583604290;N:936053", 74, 74, null, null, 596021076, 439789413, 451992691, 583604290, 936053, "ERX3851414", "ERS4266438", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.94263, 0.94098, 0.04804, 0.04844, 0.75797, 0.76039, 0.50847, 0.5014, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9782, "ERR3838747", "ERX3851413", "ERS4266437", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma High rep1", "SAMEA6501988", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501988|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep1|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma High rep1 p", "Soma High rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "Somatic_High_rep1_R1.fastq.gz Somatic_High_rep1_R2.fastq.gz", "fastq fastq", 6013555644.0, 40662218.0, "E MTAB 8707:Somatic High rep1 R", "0:73.94 1:73.95", "A:1821348300;C:1185534582;G:1227848010;T:1774836657;N:3988095", 73, 73, null, null, 1821348300, 1185534582, 1227848010, 1774836657, 3988095, "ERX3851413", "ERS4266437", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93539, 0.9357, 0.07066, 0.07028, 0.76197, 0.76386, 0.54301, 0.54343, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9783, "ERR3838746", "ERX3851412", "ERS4266436", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma dome rep2", "SAMEA6501987", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501987|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep2|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma dome rep2 p", "Soma dome rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S10_R1.fastq.gz S10_R2.fastq.gz", "fastq fastq", 1086124503.0, 7272505.0, "E MTAB 8707:S10 R", "0:74.67 1:74.68", "A:305920447;C:235855931;G:243442186;T:300439294;N:466645", 74, 74, null, null, 305920447, 235855931, 243442186, 300439294, 466645, "ERX3851412", "ERS4266436", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.94089, 0.94085, 0.04872, 0.04916, 0.7419, 0.74355, 0.51209, 0.5119, 74, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9784, "ERR3838745", "ERX3851411", "ERS4266435", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma dome rep1", "SAMEA6501986", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501986|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep1|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma dome rep1 p", "Soma dome rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S8_R1.fastq.gz S8_R2.fastq.gz", "fastq fastq", 336100162.0, 2240589.0, "E MTAB 8707:S8 R", "0:75.00 1:75.00", "A:93960580;C:73499585;G:75981355;T:92580945;N:77697", 75, 75, null, null, 93960580, 73499585, 75981355, 92580945, 77697, "ERX3851411", "ERS4266435", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93874, 0.93856, 0.05265, 0.0517, 0.74188, 0.74381, 0.51181, 0.51086, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9785, "ERR3838744", "ERX3851410", "ERS4266434", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma 256 cell rep2", "SAMEA6501985", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501985|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma 256 cell rep2 p", "Soma 256 cell rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S2_R1.fastq.gz S2_R2.fastq.gz", "fastq fastq", 1272080863.0, 8551103.0, "E MTAB 8707:S2 R", "0:74.38 1:74.38", "A:364033393;C:268850689;G:276270908;T:362172455;N:753418", 74, 74, null, null, 364033393, 268850689, 276270908, 362172455, 753418, "ERX3851410", "ERS4266434", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.80562, 0.80436, 0.23702, 0.23786, 0.77914, 0.77991, 0.51225, 0.5092, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9786, "ERR3838743", "ERX3851409", "ERS4266433", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma 256 cell rep1", "SAMEA6501984", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501984|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma 256 cell rep1 p", "Soma 256 cell rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "Somatic_256_rep1_R1.fastq.gz Somatic_256_rep1_R2.fastq.gz", "fastq fastq", 2254901578.0, 15144857.0, "E MTAB 8707:Somatic 256 rep1 R", "0:74.44 1:74.45", "A:648357135;C:475813294;G:492914743;T:636658631;N:1157775", 74, 74, null, null, 648357135, 475813294, 492914743, 636658631, 1157775, "ERX3851409", "ERS4266433", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92992, 0.92787, 0.07245, 0.07214, 0.7599, 0.76084, 0.53758, 0.53839, 74, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9787, "ERR3838742", "ERX3851408", "ERS4266432", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma 10somites rep2", "SAMEA6501983", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501983|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep2|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma 10somites rep2 p", "Soma 10somites rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S6_R1.fastq.gz S6_R2.fastq.gz", "fastq fastq", 1244080980.0, 8338002.0, "E MTAB 8707:S6 R", "0:74.60 1:74.60", "A:356418931;C:263292901;G:270630630;T:353140798;N:597720", 74, 74, null, null, 356418931, 263292901, 270630630, 353140798, 597720, "ERX3851408", "ERS4266432", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.86791, 0.86732, 0.20223, 0.20398, 0.75588, 0.75883, 0.4862, 0.48313, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [9788, "ERR3838741", "ERX3851407", "ERS4266431", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Soma 10somites rep1", "SAMEA6501982", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501982|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep1|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:Soma 10somites rep1 p", "Soma 10somites rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S4_R1.fastq.gz S4_R2.fastq.gz", "fastq fastq", 946153328.0, 6354843.0, "E MTAB 8707:S4 R", "0:74.44 1:74.45", "A:268310887;C:203457903;G:208969410;T:264875129;N:539999", 74, 74, null, null, 268310887, 203457903, 208969410, 264875129, 539999, "ERX3851407", "ERS4266431", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92415, 0.92372, 0.12138, 0.12268, 0.74061, 0.74422, 0.47246, 0.47448, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [9789, "ERR3838740", "ERX3851406", "ERS4266430", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC prim5 wt rep2", "SAMEA6501981", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501981|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC prim5 wt rep2 p", "PGC prim5 wt rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "PGC_prim5_rep2_R1.fastq.gz PGC_prim5_rep2_R2.fastq.gz", "fastq fastq", 2236371655.0, 15023634.0, "E MTAB 8707:PGC prim5 rep2 R", "0:74.43 1:74.43", "A:619039687;C:495191024;G:509021767;T:611885185;N:1233992", 74, 74, null, null, 619039687, 495191024, 509021767, 611885185, 1233992, "ERX3851406", "ERS4266430", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93137, 0.92838, 0.23991, 0.24045, 0.71435, 0.71591, 0.49054, 0.49302, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9790, "ERR3838739", "ERX3851405", "ERS4266429", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC prim5 wt rep1", "SAMEA6501980", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501980|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC prim5 wt rep1 p", "PGC prim5 wt rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "PGC_prim5_rep1_R1.fastq.gz PGC_prim5_rep1_R2.fastq.gz", "fastq fastq", 1619398294.0, 10873533.0, "E MTAB 8707:PGC prim5 rep1 R", "0:74.46 1:74.47", "A:450612629;C:355178930;G:365650222;T:447083613;N:872900", 74, 74, null, null, 450612629, 355178930, 365650222, 447083613, 872900, "ERX3851405", "ERS4266429", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92755, 0.92901, 0.22893, 0.22952, 0.71131, 0.71372, 0.49829, 0.50019, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9791, "ERR3838738", "ERX3851404", "ERS4266428", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC prim5 Morpholino rep2", "SAMEA6501979", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501979|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC prim5 Morpholino rep2 p", "PGC prim5 Morpholino rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S13_R1.fastq.gz S13_R2.fastq.gz", "fastq fastq", 906443913.0, 6069224.0, "E MTAB 8707:S13 R", "0:74.67 1:74.68", "A:256935983;C:195137600;G:200975999;T:253026767;N:367564", 74, 74, null, null, 256935983, 195137600, 200975999, 253026767, 367564, "ERX3851404", "ERS4266428", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93468, 0.93605, 0.09793, 0.09817, 0.71163, 0.71291, 0.48766, 0.48921, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9792, "ERR3838737", "ERX3851403", "ERS4266427", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC prim5 Morpholino rep1", "SAMEA6501978", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501978|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC prim5 Morpholino rep1 p", "PGC prim5 Morpholino rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "Fabio_cat_11_R1.fastq.gz Fabio_cat_11_R2.fastq.gz", "fastq fastq", 1078919524.0, 7241200.0, "E MTAB 8707:Fabio cat 11 R", "0:74.50 1:74.50", "A:308200726;C:229836659;G:236649504;T:303673221;N:559414", 74, 74, null, null, 308200726, 229836659, 236649504, 303673221, 559414, "ERX3851403", "ERS4266427", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93808, 0.93753, 0.10449, 0.10446, 0.70733, 0.71017, 0.48103, 0.48247, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9793, "ERR3838736", "ERX3851402", "ERS4266426", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC prim5 5mismatch Morpholino rep2", "SAMEA6501977", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501977|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC prim5 5mismatch Morpholino rep2 p", "PGC prim5 5mismatch Morpholino rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S17_R1.fastq.gz S17_R2.fastq.gz", "fastq fastq", 673911944.0, 4501723.0, "E MTAB 8707:S17 R", "0:74.85 1:74.85", "A:184466911;C:150779527;G:155693395;T:182720480;N:251631", 74, 74, null, null, 184466911, 150779527, 155693395, 182720480, 251631, "ERX3851402", "ERS4266426", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.9199, 0.92023, 0.08791, 0.08923, 0.70132, 0.70378, 0.49183, 0.49425, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9794, "ERR3838735", "ERX3851401", "ERS4266425", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC prim5 5mismatch Morpholino rep1", "SAMEA6501976", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501976|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC prim5 5mismatch Morpholino rep1 p", "PGC prim5 5mismatch Morpholino rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S15_R1.fastq.gz S15_R2.fastq.gz", "fastq fastq", 565636692.0, 3782000.0, "E MTAB 8707:S15 R", "0:74.78 1:74.78", "A:157353454;C:124504476;G:128260137;T:155314004;N:204621", 74, 74, null, null, 157353454, 124504476, 128260137, 155314004, 204621, "ERX3851401", "ERS4266425", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.91956, 0.91996, 0.08306, 0.08458, 0.69982, 0.70203, 0.48525, 0.48771, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [9795, "ERR3838734", "ERX3851400", "ERS4266424", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC High rep2", "SAMEA6501975", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501975|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep2|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC High rep2 p", "PGC High rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "PGC_High_rep2_R1.fastq.gz PGC_High_rep2_R2.fastq.gz", "fastq fastq", 2491013839.0, 16740632.0, "E MTAB 8707:PGC High rep2 R", "0:74.40 1:74.40", "A:715637079;C:527451931;G:545855323;T:700774175;N:1295331", 74, 74, null, null, 715637079, 527451931, 545855323, 700774175, 1295331, "ERX3851400", "ERS4266424", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93381, 0.93556, 0.06095, 0.06172, 0.76094, 0.76364, 0.52942, 0.53118, 74, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9796, "ERR3838733", "ERX3851399", "ERS4266423", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC High rep1", "SAMEA6501974", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501974|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep1|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC High rep1 p", "PGC High rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "PGC_High_rep1_R1.fastq.gz PGC_High_rep1_R2.fastq.gz", "fastq fastq", 2055218051.0, 13801653.0, "E MTAB 8707:PGC High rep1 R", "0:74.45 1:74.46", "A:594747301;C:431446277;G:445665283;T:582330624;N:1028566", 74, 74, null, null, 594747301, 431446277, 445665283, 582330624, 1028566, "ERX3851399", "ERS4266423", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93644, 0.93494, 0.06937, 0.07015, 0.76353, 0.7653, 0.45909, 0.44979, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9797, "ERR3838732", "ERX3851398", "ERS4266422", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC dome rep2", "SAMEA6501973", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501973|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep2|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC dome rep2 p", "PGC dome rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S9_R1.fastq.gz S9_R2.fastq.gz", "fastq fastq", 882858901.0, 5912255.0, "E MTAB 8707:S9 R", "0:74.66 1:74.67", "A:246639630;C:193554406;G:199940889;T:242369366;N:354610", 74, 74, null, null, 246639630, 193554406, 199940889, 242369366, 354610, "ERX3851398", "ERS4266422", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.94045, 0.9404, 0.04635, 0.04658, 0.74582, 0.74777, 0.4915, 0.49248, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9798, "ERR3838731", "ERX3851397", "ERS4266421", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC dome rep1", "SAMEA6501972", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501972|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep1|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC dome rep1 p", "PGC dome rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S7_R1.fastq.gz S7_R2.fastq.gz", "fastq fastq", 592299285.0, 3961989.0, "E MTAB 8707:S7 R", "0:74.75 1:74.75", "A:166664600;C:128421892;G:132787149;T:164189412;N:236232", 74, 74, null, null, 166664600, 128421892, 132787149, 164189412, 236232, "ERX3851397", "ERS4266421", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93981, 0.94032, 0.04868, 0.04843, 0.74627, 0.74722, 0.49243, 0.48872, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9799, "ERR3838730", "ERX3851396", "ERS4266420", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC 256 cell rep2", "SAMEA6501971", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501971|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC 256 cell rep2 p", "PGC 256 cell rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S1_R1.fastq.gz S1_R2.fastq.gz", "fastq fastq", 745277323.0, 4983607.0, "E MTAB 8707:S1 R", "0:74.77 1:74.77", "A:208352741;C:163024343;G:168234953;T:205391192;N:274094", 74, 74, null, null, 208352741, 163024343, 168234953, 205391192, 274094, "ERX3851396", "ERS4266420", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.9393, 0.9395, 0.03941, 0.03941, 0.75473, 0.75708, 0.51338, 0.51754, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9800, "ERR3838729", "ERX3851395", "ERS4266419", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC 256 cell rep1", "SAMEA6501970", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501970|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC 256 cell rep1 p", "PGC 256 cell rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "PGC_256_rep1_R1.fastq.gz PGC_256_rep1_R2.fastq.gz", "fastq fastq", 1876891175.0, 12625794.0, "E MTAB 8707:PGC 256 rep1 R", "0:74.32 1:74.33", "A:539140549;C:396392844;G:411568412;T:528672735;N:1116635", 74, 74, null, null, 539140549, 396392844, 411568412, 528672735, 1116635, "ERX3851395", "ERS4266419", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.92251, 0.92173, 0.06705, 0.06723, 0.76059, 0.76374, 0.54467, 0.54135, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [9801, "ERR3838728", "ERX3851394", "ERS4266418", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC 10somites rep2", "SAMEA6501969", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501969|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep2|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC 10somites rep2 p", "PGC 10somites rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S5_R1.fastq.gz S5_R2.fastq.gz", "fastq fastq", 1186993033.0, 7958634.0, "E MTAB 8707:S5 R", "0:74.57 1:74.58", "A:332263881;C:259239478;G:267014990;T:327946611;N:528073", 74, 74, null, null, 332263881, 259239478, 267014990, 327946611, 528073, "ERX3851394", "ERS4266418", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.90713, 0.9062, 0.10071, 0.1016, 0.73058, 0.73279, 0.48458, 0.48038, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [9802, "ERR3838727", "ERX3851393", "ERS4266417", "ERP119601", "PRJEB36411", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-8707", "Transcriptome Analysis", "Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC 10somites rep1", "SAMEA6501968", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501968|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep1|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 8707:PGC 10somites rep1 p", "PGC 10somites rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell", "OTHER", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP119601", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24", "S3_R1.fastq.gz S3_R2.fastq.gz", "fastq fastq", 1230551446.0, 8251644.0, "E MTAB 8707:S3 R", "0:74.56 1:74.57", "A:345409587;C:267720436;G:275626594;T:341185818;N:609011", 74, 74, null, null, 345409587, 267720436, 275626594, 341185818, 609011, "ERX3851393", "ERS4266417", "ERA2354529", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.90983, 0.90985, 0.1005, 0.10037, 0.72622, 0.72825, 0.49116, 0.49135, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-01-24", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [10111, "ERR4911024", "ERX4777847", "ERS5435613", "ERP125516", "PRJEB41701", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-9857", "Transcriptome Analysis", "In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC Rescue rep2", "SAMEA7678632", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678632|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep2|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 9857:PGC Rescue rep2 p", "PGC Rescue rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP125516", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09", "Tdrd7_Rescue_PGC_rep2_R1.fastq.gz Tdrd7_Rescue_PGC_rep2_R2.fastq.gz", "fastq fastq", 6487121744.0, 43103086.0, "E MTAB 9857:Tdrd7 Rescue PGC rep2 R", "0:75.26 1:75.24", "A:1769293880;C:1469053016;G:1516553427;T:1729496045;N:2725376", 75, 75, null, null, 1769293880, 1469053016, 1516553427, 1729496045, 2725376, "ERX4777847", "ERS5435613", "ERA3184570", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.95185, 0.95349, 0.04302, 0.04315, 0.72829, 0.73022, 0.47176, 0.47104, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [10112, "ERR4911023", "ERX4777846", "ERS5435612", "ERP125516", "PRJEB41701", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-9857", "Transcriptome Analysis", "In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC Rescue rep1", "SAMEA7678631", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678631|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep1|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 9857:PGC Rescue rep1 p", "PGC Rescue rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP125516", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09", "Tdrd7_Rescue_PGC_rep1_R1.fastq.gz Tdrd7_Rescue_PGC_rep1_R2.fastq.gz", "fastq fastq", 5952473889.0, 39454929.0, "E MTAB 9857:Tdrd7 Rescue PGC rep1 R", "0:75.44 1:75.43", "A:1640467527;C:1332668425;G:1380033115;T:1597665169;N:1639653", 75, 75, null, null, 1640467527, 1332668425, 1380033115, 1597665169, 1639653, "ERX4777846", "ERS5435612", "ERA3184570", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.95086, 0.95226, 0.06292, 0.0629, 0.70341, 0.70579, 0.46524, 0.46691, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [10113, "ERR4911022", "ERX4777845", "ERS5435611", "ERP125516", "PRJEB41701", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-9857", "Transcriptome Analysis", "In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC MO rep2", "SAMEA7678630", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678630|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep2|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 9857:PGC MO rep2 p", "PGC MO rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: compound:tdrd7 targeting MO", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP125516", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09", "Tdrd7_MO_PGC_rep2_R1.fastq.gz Tdrd7_MO_PGC_rep2_R2.fastq.gz", "fastq fastq", 906443913.0, 6069224.0, "E MTAB 9857:Tdrd7 MO PGC rep2 R", "0:74.67 1:74.68", "A:256935983;C:195137600;G:200975999;T:253026767;N:367564", 74, 74, null, null, 256935983, 195137600, 200975999, 253026767, 367564, "ERX4777845", "ERS5435611", "ERA3184570", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.93468, 0.93603, 0.09796, 0.09848, 0.7119, 0.71439, 0.48682, 0.48933, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [10114, "ERR4911021", "ERX4777844", "ERS5435610", "ERP125516", "PRJEB41701", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-9857", "Transcriptome Analysis", "In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC MO rep1", "SAMEA7678629", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678629|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep1|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 9857:PGC MO rep1 p", "PGC MO rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: compound:tdrd7 targeting MO", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP125516", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09", "Tdrd7_MO_PGC_rep1_R1.fastq.gz Tdrd7_MO_PGC_rep1_R2.fastq.gz", "fastq fastq", 1078919524.0, 7241200.0, "E MTAB 9857:Tdrd7 MO PGC rep1 R", "0:74.50 1:74.50", "A:308200726;C:229836659;G:236649504;T:303673221;N:559414", 74, 74, null, null, 308200726, 229836659, 236649504, 303673221, 559414, "ERX4777844", "ERS5435610", "ERA3184570", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.938, 0.93748, 0.10463, 0.10431, 0.7077, 0.70999, 0.48098, 0.48239, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [10115, "ERR4911020", "ERX4777843", "ERS5435609", "ERP125516", "PRJEB41701", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-9857", "Transcriptome Analysis", "In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC 5mm rep2", "SAMEA7678628", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678628|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep2|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 9857:PGC 5mm rep2 p", "PGC 5mm rep2 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: compound:tdrd7 5mismatch MO", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP125516", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09", "Tdrd7_5mm_PGC_rep2_R1.fastq.gz Tdrd7_5mm_PGC_rep2_R2.fastq.gz", "fastq fastq", 673911944.0, 4501723.0, "E MTAB 9857:Tdrd7 5mm PGC rep2 R", "0:74.85 1:74.85", "A:184466911;C:150779527;G:155693395;T:182720480;N:251631", 74, 74, null, null, 184466911, 150779527, 155693395, 182720480, 251631, "ERX4777843", "ERS5435609", "ERA3184570", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.91989, 0.92025, 0.08795, 0.08919, 0.70096, 0.70416, 0.49184, 0.49415, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [10116, "ERR4911019", "ERX4777842", "ERS5435608", "ERP125516", "PRJEB41701", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E-MTAB-9857", "Transcriptome Analysis", "In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02", null, "Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "PGC 5mm rep1", "SAMEA7678627", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK", "ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678627|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep1|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "E MTAB 9857:PGC 5mm rep1 p", "PGC 5mm rep1 p", "RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 \u03bcm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/\u03bcl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.", "Experimental Factor: compound:tdrd7 5mismatch MO", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP125516", "NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis", "ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09", "Tdrd7_5mm_PGC_rep1_R1.fastq.gz Tdrd7_5mm_PGC_rep1_R2.fastq.gz", "fastq fastq", 565636692.0, 3782000.0, "E MTAB 9857:Tdrd7 5mm PGC rep1 R", "0:74.78 1:74.78", "A:157353454;C:124504476;G:128260137;T:155314004;N:204621", 74, 74, null, null, 157353454, 124504476, 128260137, 155314004, 204621, "ERX4777842", "ERS5435608", "ERA3184570", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", "MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive", 2, 0.91957, 0.91995, 0.08301, 0.0845, 0.69929, 0.70195, 0.48544, 0.4877, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2020-12-02", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [50527, "SRR8129710", "SRX4950832", "SRS3993023", "SRP167139", "PRJNA499073", "Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes", "GSE121917", "Transcriptome Analysis", "We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.", null, "pubmed:30894119", null, "Rneasy unsorted", "GSM3449971", null, "tissue:Fli:GFP  whole embryo 5 days  RNeasy  sample 1|cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNeasy plus micro kit", "Rneasy unsorted", "Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data", "Fli:GFP  whole embryo 5 days  RNeasy  sample 1", null, "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", null, "cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNeasy plus micro kit", "GSM3449971", "GSM3449971: Rneasy unsorted; Danio rerio; RNA Seq", "GSM3449971", null, "1", "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", "GEO Accession:GSM3449971", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP167139", null, null, "Q_unsorted_R1.fastq.gz Q_unsorted_R2.fastq.gz", "fastq fastq", 4155128139.0, 27505173.0, "GSM3449971 r1", "0:75.53 1:75.53", "A:1075371555;C:1005905830;G:1019395949;T:1054443500;N:11305", 75, 75, null, null, 1075371555, 1005905830, 1019395949, 1054443500, 11305, "SRX4950832", "SRS3993023", "SRA800291", "GEO", "Center for Medical Genetics, Ghent University", 2, 0.92688, 0.92569, 0.06942, 0.0708, 0.73241, 0.74164, 0.44144, 0.44652, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2018-10-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [50528, "SRR8129709", "SRX4950831", "SRS3993022", "SRP167139", "PRJNA499073", "Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes", "GSE121917", "Transcriptome Analysis", "We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.", null, "pubmed:30894119", null, "RNAqueous unsorted", "GSM3449970", null, "tissue:Fli:GFP  whole embryo 5 days  RNAqueous  sample 1|cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNAqueous micro", "RNAqueous unsorted", "Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data", "Fli:GFP  whole embryo 5 days  RNAqueous  sample 1", null, "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", null, "cell type:fli:GFP  whole embryo|age:5 days|rna isolation kit:RNAqueous micro", "GSM3449970", "GSM3449970: RNAqueous unsorted; Danio rerio; RNA Seq", "GSM3449970", null, "1", "polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina", "GEO Accession:GSM3449970", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP167139", null, null, "A_unsorted_R1.fastq.gz A_unsorted_R2.fastq.gz", "fastq fastq", 3613198121.0, 23920751.0, "GSM3449970 r1", "0:75.53 1:75.52", "A:976322858;C:832409562;G:835538411;T:968916959;N:10331", 75, 75, null, null, 976322858, 832409562, 835538411, 968916959, 10331, "SRX4950831", "SRS3993022", "SRA800291", "GEO", "Center for Medical Genetics, Ghent University", 2, 0.91518, 0.91772, 0.12399, 0.12715, 0.71196, 0.71764, 0.46555, 0.45805, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2018-10-29", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [51258, "SRR8632327", "SRX5431028", "SRS4411023", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "total rep 3", "GSM3629722", null, "source name:whole embryo|strain background:AB|gentoype/variation:wild type|tissue:whole embryo", "total rep 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "whole embryo", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:wild type|tissue:whole embryo", "GSM3629722", "GSM3629722: total rep 3; Danio rerio; RNA Seq", "GSM3629722", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629722", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP186864", null, null, "c3.fastq.gz", "fastq", 142798100.0, 2855962.0, "GSM3629722 r1", "0:50", "A:33558108;C:34453721;G:38902032;T:35874180;N:10059", 50, null, null, null, 33558108, 34453721, 38902032, 35874180, 10059, "SRX5431028", "SRS4411023", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 1, 0.02673, null, 0.00469, null, 0.98455, null, 0.62342, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [51259, "SRR8632326", "SRX5431027", "SRS4411022", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "total rep 2", "GSM3629721", null, "source name:whole embryo|strain background:AB|gentoype/variation:wild type|tissue:whole embryo", "total rep 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "whole embryo", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:wild type|tissue:whole embryo", "GSM3629721", "GSM3629721: total rep 2; Danio rerio; RNA Seq", "GSM3629721", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629721", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP186864", null, null, "c2.fastq.gz", "fastq", 176136650.0, 3522733.0, "GSM3629721 r1", "0:50", "A:42179466;C:41890753;G:47676052;T:44377787;N:12592", 50, null, null, null, 42179466, 41890753, 47676052, 44377787, 12592, "SRX5431027", "SRS4411022", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 1, 0.01253, null, 0.00298, null, 0.99342, null, 0.67131, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [51260, "SRR8632325", "SRX5431026", "SRS4411021", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "total rep 1", "GSM3629720", null, "source name:whole embryo|strain background:AB|gentoype/variation:wild type|tissue:whole embryo", "total rep 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "whole embryo", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:wild type|tissue:whole embryo", "GSM3629720", "GSM3629720: total rep 1; Danio rerio; RNA Seq", "GSM3629720", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP186864", null, null, "c1.fastq.gz", "fastq", 180216500.0, 3604330.0, "GSM3629720 r1", "0:50", "A:43005950;C:42787875;G:49009406;T:45400170;N:13099", 50, null, null, null, 43005950, 42787875, 49009406, 45400170, 13099, "SRX5431026", "SRS4411021", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 1, 0.01759, null, 0.00459, null, 0.99101, null, 0.71252, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52380, "SRR9198634", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A10_R1.fastq.gz", "fastq", 22730187.0, 528609.0, "GSM3851760 r1", "0:43", "A:6531713;C:4702880;G:4826497;T:6669097;N:0", 43, null, null, null, 6531713, 4702880, 4826497, 6669097, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86984, null, 0.3317, null, 0.86977, null, 0.50211, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52381, "SRR9198635", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A19_R1.fastq.gz", "fastq", 25422417.0, 591219.0, "GSM3851760 r10", "0:43", "A:7420297;C:5115508;G:5236996;T:7649616;N:0", 43, null, null, null, 7420297, 5115508, 5236996, 7649616, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85285, null, 0.39693, null, 0.87675, null, 0.44071, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52382, "SRR9198636", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E13_R1.fastq.gz", "fastq", 34049550.0, 791850.0, "GSM3851760 r100", "0:43", "A:9807395;C:7041091;G:7187781;T:10013283;N:0", 43, null, null, null, 9807395, 7041091, 7187781, 10013283, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86073, null, 0.36367, null, 0.85589, null, 0.48001, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52383, "SRR9198637", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E14_R1.fastq.gz", "fastq", 30226893.0, 702951.0, "GSM3851760 r101", "0:43", "A:8402351;C:6582983;G:6770609;T:8470950;N:0", 43, null, null, null, 8402351, 6582983, 6770609, 8470950, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87786, null, 0.20548, null, 0.92119, null, 0.5325, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52384, "SRR9198638", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E15_R1.fastq.gz", "fastq", 31104093.0, 723351.0, "GSM3851760 r102", "0:43", "A:8946868;C:6414234;G:6568361;T:9174630;N:0", 43, null, null, null, 8946868, 6414234, 6568361, 9174630, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85741, null, 0.37503, null, 0.89073, null, 0.48996, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52385, "SRR9198639", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E16_R1.fastq.gz", "fastq", 34438399.0, 800893.0, "GSM3851760 r103", "0:43", "A:9959668;C:7061544;G:7228493;T:10188694;N:0", 43, null, null, null, 9959668, 7061544, 7228493, 10188694, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85657, null, 0.37381, null, 0.89503, null, 0.47367, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52386, "SRR9198640", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E17_R1.fastq.gz", "fastq", 31687560.0, 736920.0, "GSM3851760 r104", "0:43", "A:9042349;C:6631079;G:6783803;T:9230329;N:0", 43, null, null, null, 9042349, 6631079, 6783803, 9230329, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86922, null, 0.28531, null, 0.87647, null, 0.50906, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52387, "SRR9198641", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E18_R1.fastq.gz", "fastq", 28829178.0, 670446.0, "GSM3851760 r105", "0:43", "A:8040858;C:6240958;G:6375940;T:8171422;N:0", 43, null, null, null, 8040858, 6240958, 6375940, 8171422, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.88484, null, 0.25108, null, 0.89796, null, 0.52328, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52388, "SRR9198642", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E19_R1.fastq.gz", "fastq", 29456161.0, 685027.0, "GSM3851760 r106", "0:43", "A:8185810;C:6362322;G:6490611;T:8417418;N:0", 43, null, null, null, 8185810, 6362322, 6490611, 8417418, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87467, null, 0.2568, null, 0.87637, null, 0.44643, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52389, "SRR9198643", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E1_R1.fastq.gz", "fastq", 41009788.0, 953716.0, "GSM3851760 r107", "0:43", "A:11633133;C:8565119;G:8761780;T:12049756;N:0", 43, null, null, null, 11633133, 8565119, 8761780, 12049756, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83802, null, 0.32341, null, 0.88038, null, 0.49748, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52390, "SRR9198644", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E20_R1.fastq.gz", "fastq", 29314777.0, 681739.0, "GSM3851760 r108", "0:43", "A:8470707;C:6002913;G:6136651;T:8704506;N:0", 43, null, null, null, 8470707, 6002913, 6136651, 8704506, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85476, null, 0.37692, null, 0.87633, null, 0.47456, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52391, "SRR9198645", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E21_R1.fastq.gz", "fastq", 39374455.0, 915685.0, "GSM3851760 r109", "0:43", "A:11315860;C:8119631;G:8323167;T:11615797;N:0", 43, null, null, null, 11315860, 8119631, 8323167, 11615797, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85391, null, 0.36988, null, 0.91039, null, 0.50229, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52392, "SRR9198646", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A1_R1.fastq.gz", "fastq", 3574031.0, 83117.0, "GSM3851760 r11", "0:43", "A:1037490;C:644669;G:647675;T:1244197;N:0", 43, null, null, null, 1037490, 644669, 647675, 1244197, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.08124, null, 0.07796, null, 0.99709, null, 0.43644, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52393, "SRR9198647", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E22_R1.fastq.gz", "fastq", 45159546.0, 1050222.0, "GSM3851760 r110", "0:43", "A:13081668;C:9210038;G:9426293;T:13441547;N:0", 43, null, null, null, 13081668, 9210038, 9426293, 13441547, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.84853, null, 0.41231, null, 0.90678, null, 0.50893, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52394, "SRR9198648", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E23_R1.fastq.gz", "fastq", 46674522.0, 1085454.0, "GSM3851760 r111", "0:43", "A:13407038;C:9644708;G:9870254;T:13752522;N:0", 43, null, null, null, 13407038, 9644708, 9870254, 13752522, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.8528, null, 0.35087, null, 0.91896, null, 0.50728, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52395, "SRR9198649", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E24_R1.fastq.gz", "fastq", 40946578.0, 952246.0, "GSM3851760 r112", "0:43", "A:11353999;C:8901776;G:9087747;T:11603056;N:0", 43, null, null, null, 11353999, 8901776, 9087747, 11603056, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.88574, null, 0.2555, null, 0.89203, null, 0.53214, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52396, "SRR9198650", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E2_R1.fastq.gz", "fastq", 35795909.0, 832463.0, "GSM3851760 r113", "0:43", "A:10008515;C:7658565;G:7846504;T:10282325;N:0", 43, null, null, null, 10008515, 7658565, 7846504, 10282325, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.8507, null, 0.24931, null, 0.87643, null, 0.51656, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52397, "SRR9198651", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E3_R1.fastq.gz", "fastq", 34867496.0, 810872.0, "GSM3851760 r114", "0:43", "A:9952111;C:7269477;G:7461395;T:10184513;N:0", 43, null, null, null, 9952111, 7269477, 7461395, 10184513, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85806, null, 0.33604, null, 0.85468, null, 0.48609, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52398, "SRR9198652", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E4_R1.fastq.gz", "fastq", 4629036.0, 107652.0, "GSM3851760 r115", "0:43", "A:1294799;C:1008604;G:1044853;T:1280780;N:0", 43, null, null, null, 1294799, 1008604, 1044853, 1280780, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87228, null, 0.19931, null, 0.94229, null, 0.54841, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52399, "SRR9198653", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E5_R1.fastq.gz", "fastq", 6320914.0, 146998.0, "GSM3851760 r116", "0:43", "A:1861194;C:1147340;G:1160856;T:2151524;N:0", 43, null, null, null, 1861194, 1147340, 1160856, 2151524, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.0887, null, 0.08394, null, 0.99389, null, 0.4262, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52400, "SRR9198654", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E6_R1.fastq.gz", "fastq", 32168257.0, 748099.0, "GSM3851760 r117", "0:43", "A:9360276;C:6476288;G:6645427;T:9686266;N:0", 43, null, null, null, 9360276, 6476288, 6645427, 9686266, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83653, null, 0.4296, null, 0.91171, null, 0.48995, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52401, "SRR9198655", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E7_R1.fastq.gz", "fastq", 36882089.0, 857723.0, "GSM3851760 r118", "0:43", "A:10430067;C:7805495;G:7991940;T:10654587;N:0", 43, null, null, null, 10430067, 7805495, 7991940, 10654587, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86871, null, 0.29809, null, 0.90011, null, 0.49514, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52402, "SRR9198656", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E8_R1.fastq.gz", "fastq", 24809839.0, 576973.0, "GSM3851760 r119", "0:43", "A:7144307;C:5119783;G:5223795;T:7321954;N:0", 43, null, null, null, 7144307, 5119783, 5223795, 7321954, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86137, null, 0.37732, null, 0.88611, null, 0.49645, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52403, "SRR9198657", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A20_R1.fastq.gz", "fastq", 20992729.0, 488203.0, "GSM3851760 r12", "0:43", "A:6046890;C:4289153;G:4410467;T:6246219;N:0", 43, null, null, null, 6046890, 4289153, 4410467, 6246219, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85185, null, 0.31773, null, 0.91845, null, 0.58528, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52404, "SRR9198658", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "E9_R1.fastq.gz", "fastq", 40215105.0, 935235.0, "GSM3851760 r120", "0:43", "A:11360646;C:8521492;G:8730341;T:11602626;N:0", 43, null, null, null, 11360646, 8521492, 8730341, 11602626, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86307, null, 0.33177, null, 0.8982, null, 0.47644, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52405, "SRR9198659", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F10_R1.fastq.gz", "fastq", 19107093.0, 444351.0, "GSM3851760 r121", "0:43", "A:5563356;C:3848064;G:3951297;T:5744376;N:0", 43, null, null, null, 5563356, 3848064, 3951297, 5744376, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.84285, null, 0.40366, null, 0.89171, null, 0.48828, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52406, "SRR9198660", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F11_R1.fastq.gz", "fastq", 31628951.0, 735557.0, "GSM3851760 r122", "0:43", "A:9033354;C:6606929;G:6787882;T:9200786;N:0", 43, null, null, null, 9033354, 6606929, 6787882, 9200786, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86464, null, 0.31248, null, 0.90104, null, 0.50525, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52407, "SRR9198661", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F12_R1.fastq.gz", "fastq", 24055834.0, 559438.0, "GSM3851760 r123", "0:43", "A:6622600;C:5260253;G:5395038;T:6777943;N:0", 43, null, null, null, 6622600, 5260253, 5395038, 6777943, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87692, null, 0.2118, null, 0.91238, null, 0.42713, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52408, "SRR9198662", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F13_R1.fastq.gz", "fastq", 27688517.0, 643919.0, "GSM3851760 r124", "0:43", "A:8080865;C:5560695;G:5700222;T:8346735;N:0", 43, null, null, null, 8080865, 5560695, 5700222, 8346735, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83469, null, 0.43252, null, 0.90938, null, 0.48723, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52409, "SRR9198663", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F14_R1.fastq.gz", "fastq", 21924754.0, 509878.0, "GSM3851760 r125", "0:43", "A:6090527;C:4750408;G:4851102;T:6232717;N:0", 43, null, null, null, 6090527, 4750408, 4851102, 6232717, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.88707, null, 0.24693, null, 0.89098, null, 0.42985, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52410, "SRR9198664", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F15_R1.fastq.gz", "fastq", 24524190.0, 570330.0, "GSM3851760 r126", "0:43", "A:7099978;C:5008036;G:5144163;T:7272013;N:0", 43, null, null, null, 7099978, 5008036, 5144163, 7272013, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.84943, null, 0.37319, null, 0.88542, null, 0.49363, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52411, "SRR9198665", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F16_R1.fastq.gz", "fastq", 22940113.0, 533491.0, "GSM3851760 r127", "0:43", "A:6806189;C:4493084;G:4602856;T:7037984;N:0", 43, null, null, null, 6806189, 4493084, 4602856, 7037984, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83481, null, 0.50302, null, 0.90155, null, 0.55502, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52412, "SRR9198666", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F17_R1.fastq.gz", "fastq", 14327600.0, 333200.0, "GSM3851760 r128", "0:43", "A:4094254;C:2985444;G:3065124;T:4182778;N:0", 43, null, null, null, 4094254, 2985444, 3065124, 4182778, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86023, null, 0.27478, null, 0.9262, null, 0.50627, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52413, "SRR9198667", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F18_R1.fastq.gz", "fastq", 13237507.0, 307849.0, "GSM3851760 r129", "0:43", "A:3843212;C:2694145;G:2779980;T:3920170;N:0", 43, null, null, null, 3843212, 2694145, 2779980, 3920170, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83869, null, 0.33275, null, 0.89802, null, 0.53459, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52414, "SRR9198668", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A21_R1.fastq.gz", "fastq", 23607215.0, 549005.0, "GSM3851760 r13", "0:43", "A:6949976;C:4679980;G:4802349;T:7174910;N:0", 43, null, null, null, 6949976, 4679980, 4802349, 7174910, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.84434, null, 0.46159, null, 0.89173, null, 0.46625, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52415, "SRR9198669", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F19_R1.fastq.gz", "fastq", 28189725.0, 655575.0, "GSM3851760 r130", "0:43", "A:7998454;C:5905042;G:6043708;T:8242521;N:0", 43, null, null, null, 7998454, 5905042, 6043708, 8242521, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86503, null, 0.27006, null, 0.89465, null, 0.50557, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52416, "SRR9198670", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F1_R1.fastq.gz", "fastq", 19684712.0, 457784.0, "GSM3851760 r131", "0:43", "A:5427483;C:4337414;G:4521536;T:5398279;N:0", 43, null, null, null, 5427483, 4337414, 4521536, 5398279, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87052, null, 0.16084, null, 0.90276, null, 0.50242, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52417, "SRR9198671", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F20_R1.fastq.gz", "fastq", 25811825.0, 600275.0, "GSM3851760 r132", "0:43", "A:7620260;C:5037810;G:5184002;T:7969753;N:0", 43, null, null, null, 7620260, 5037810, 5184002, 7969753, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.81686, null, 0.50881, null, 0.91031, null, 0.52696, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52418, "SRR9198672", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F21_R1.fastq.gz", "fastq", 31327564.0, 728548.0, "GSM3851760 r133", "0:43", "A:8893372;C:6587100;G:6751304;T:9095788;N:0", 43, null, null, null, 8893372, 6587100, 6751304, 9095788, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87094, null, 0.28476, null, 0.87797, null, 0.5071, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52419, "SRR9198673", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F22_R1.fastq.gz", "fastq", 25009187.0, 581609.0, "GSM3851760 r134", "0:43", "A:6965919;C:5371799;G:5499602;T:7171867;N:0", 43, null, null, null, 6965919, 5371799, 5499602, 7171867, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87185, null, 0.25342, null, 0.91214, null, 0.56099, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52420, "SRR9198674", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F23_R1.fastq.gz", "fastq", 32902998.0, 765186.0, "GSM3851760 r135", "0:43", "A:9533499;C:6716093;G:6870853;T:9782553;N:0", 43, null, null, null, 9533499, 6716093, 6870853, 9782553, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85794, null, 0.35536, null, 0.87671, null, 0.50276, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52421, "SRR9198675", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F24_R1.fastq.gz", "fastq", 31013578.0, 721246.0, "GSM3851760 r136", "0:43", "A:9001008;C:6274940;G:6415769;T:9321861;N:0", 43, null, null, null, 9001008, 6274940, 6415769, 9321861, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.84095, null, 0.36884, null, 0.92234, null, 0.53474, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52422, "SRR9198676", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F2_R1.fastq.gz", "fastq", 23623125.0, 549375.0, "GSM3851760 r137", "0:43", "A:6462921;C:5250054;G:5397862;T:6512288;N:0", 43, null, null, null, 6462921, 5250054, 5397862, 6512288, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87991, null, 0.23553, null, 0.91173, null, 0.51346, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52423, "SRR9198677", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F3_R1.fastq.gz", "fastq", 56849268.0, 1322076.0, "GSM3851760 r138", "0:43", "A:15634028;C:12520216;G:12867754;T:15827270;N:0", 43, null, null, null, 15634028, 12520216, 12867754, 15827270, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.871, null, 0.20701, null, 0.92703, null, 0.49491, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52424, "SRR9198678", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F4_R1.fastq.gz", "fastq", 46322653.0, 1077271.0, "GSM3851760 r139", "0:43", "A:13343135;C:9581671;G:9823311;T:13574536;N:0", 43, null, null, null, 13343135, 9581671, 9823311, 13574536, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85062, null, 0.40373, null, 0.91281, null, 0.50706, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52425, "SRR9198679", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A22_R1.fastq.gz", "fastq", 25134059.0, 584513.0, "GSM3851760 r14", "0:43", "A:6909921;C:5512326;G:5635533;T:7076279;N:0", 43, null, null, null, 6909921, 5512326, 5635533, 7076279, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.89127, null, 0.19785, null, 0.90179, null, 0.50794, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52426, "SRR9198680", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F5_R1.fastq.gz", "fastq", 51033561.0, 1186827.0, "GSM3851760 r140", "0:43", "A:14605293;C:10643260;G:10917516;T:14867492;N:0", 43, null, null, null, 14605293, 10643260, 10917516, 14867492, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85584, null, 0.39713, null, 0.90043, null, 0.48754, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52427, "SRR9198681", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F6_R1.fastq.gz", "fastq", 11300916.0, 262812.0, "GSM3851760 r141", "0:43", "A:3321000;C:2297183;G:2385833;T:3296900;N:0", 43, null, null, null, 3321000, 2297183, 2385833, 3296900, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.85718, null, 0.4262, null, 0.91914, null, 0.50468, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52428, "SRR9198682", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F7_R1.fastq.gz", "fastq", 45278742.0, 1052994.0, "GSM3851760 r142", "0:43", "A:13002638;C:9369548;G:9622447;T:13284109;N:0", 43, null, null, null, 13002638, 9369548, 9622447, 13284109, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.83814, null, 0.37647, null, 0.90554, null, 0.49616, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52429, "SRR9198683", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F8_R1.fastq.gz", "fastq", 14835344.0, 345008.0, "GSM3851760 r143", "0:43", "A:4110076;C:3245754;G:3325157;T:4154357;N:0", 43, null, null, null, 4110076, 3245754, 3325157, 4154357, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86906, null, 0.19318, null, 0.89394, null, 0.51872, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52430, "SRR9198684", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "F9_R1.fastq.gz", "fastq", 22851017.0, 531419.0, "GSM3851760 r144", "0:43", "A:6468358;C:4849150;G:4966680;T:6566829;N:0", 43, null, null, null, 6468358, 4849150, 4966680, 6566829, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.8823, null, 0.18338, null, 0.88168, null, 0.4915, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52431, "SRR9198685", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G10_R1.fastq.gz", "fastq", 10655400.0, 247800.0, "GSM3851760 r145", "0:43", "A:2964578;C:2045554;G:1988943;T:3656325;N:0", 43, null, null, null, 2964578, 2045554, 1988943, 3656325, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.08282, null, 0.07443, null, 0.99553, null, 0.77115, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52432, "SRR9198686", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G11_R1.fastq.gz", "fastq", 38720210.0, 900470.0, "GSM3851760 r146", "0:43", "A:10652326;C:8557186;G:8758762;T:10751936;N:0", 43, null, null, null, 10652326, 8557186, 8758762, 10751936, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87521, null, 0.21283, null, 0.93779, null, 0.50587, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52433, "SRR9198687", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G12_R1.fastq.gz", "fastq", 37872809.0, 880763.0, "GSM3851760 r147", "0:43", "A:10570260;C:8249277;G:8452653;T:10600619;N:0", 43, null, null, null, 10570260, 8249277, 8452653, 10600619, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.88166, null, 0.24488, null, 0.87265, null, 0.47744, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52434, "SRR9198688", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G13_R1.fastq.gz", "fastq", 46220313.0, 1074891.0, "GSM3851760 r148", "0:43", "A:12943521;C:9974404;G:10197868;T:13104520;N:0", 43, null, null, null, 12943521, 9974404, 10197868, 13104520, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.86369, null, 0.28235, null, 0.90995, null, 0.5024, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52435, "SRR9198689", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G14_R1.fastq.gz", "fastq", 22452579.0, 522153.0, "GSM3851760 r149", "0:43", "A:6052976;C:5108508;G:5238826;T:6052269;N:0", 43, null, null, null, 6052976, 5108508, 5238826, 6052269, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.89425, null, 0.12262, null, 0.91234, null, 0.51154, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52436, "SRR9198690", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "A23_R1.fastq.gz", "fastq", 11064115.0, 257305.0, "GSM3851760 r15", "0:43", "A:3312117;C:2015333;G:2092587;T:3644078;N:0", 43, null, null, null, 3312117, 2015333, 2092587, 3644078, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.67131, null, 0.56353, null, 0.94596, null, 0.46246, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52437, "SRR9198691", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G15_R1.fastq.gz", "fastq", 26636608.0, 619456.0, "GSM3851760 r150", "0:43", "A:7482453;C:5765357;G:5930514;T:7458284;N:0", 43, null, null, null, 7482453, 5765357, 5930514, 7458284, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.88297, null, 0.26878, null, 0.85979, null, 0.47992, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52438, "SRR9198692", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G16_R1.fastq.gz", "fastq", 38014150.0, 884050.0, "GSM3851760 r151", "0:43", "A:10576888;C:8304761;G:8506878;T:10625623;N:0", 43, null, null, null, 10576888, 8304761, 8506878, 10625623, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.87683, null, 0.25851, null, 0.89767, null, 0.48845, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52439, "SRR9198693", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G17_R1.fastq.gz", "fastq", 40972507.0, 952849.0, "GSM3851760 r152", "0:43", "A:11958245;C:8186722;G:8404224;T:12423316;N:0", 43, null, null, null, 11958245, 8186722, 8404224, 12423316, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.79842, null, 0.48846, null, 0.93277, null, 0.51012, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52440, "SRR9198694", "SRX5970646", "SRS4876620", "SRP200391", "PRJNA546235", "Functionally distinct subgroups of Oligodendrocyte precursor cells integrate neural activity and execute myelin formation", "GSE132166", "Other", "Neuronal activity can regulate the formation of new myelin by controlling division and differentiation of oligodendrocyte precursor cells OPCs. If activity directly instructs OPCs to differentiate or whether this process underlies a more complex regulation in unclear  because it is not known if OPCs with different functions exist. By following lineage formation of individual OPC clones  single cell RNA sequencing  in vivo calcium imaging and manipulation of neural activity  we show that OPCs in the zebrafish spinal cord can be divided into two functional entities. One subgroup forms elaborate process networks and exhibits a high degree of calcium signalling activity  but infrequently differentiates  despite contact with permissive axons. Instead  these OPCs can divide in an activity and calcium dependent manner to produce another subgroup of OPCs  which readily differentiates and which shows less elaborate  more dynamic processes  and less calcium signaling activity. Our data reveal functional diversity within the OPC population in responding to neural activity and show that activity regulates proliferation of a subset of OPCs that is distinct from the cells that will differentiate  with implications for myelin development  plasticity  and repair. Overall design: Single cell RNA sequencing from zebrafish with genetically labelled Oligodendrocyte Precursor Cells was carried out to reveal the genetic heterogeneity of this population. The transcriptomic data will be supplemented with RNA in situ hybridization and immunofluorescence stainings to validate candidate markers of subopulations  and in vivo live cell imaging data to map cell fates.  Oligodendrocyte Precursor Cells from Tgolig1:memEYFP transgenic zebrafish at 5 dpf were FACS sorted in 384 well plated containing cell lysis buffer and subsequently processed for SmartSeq2", null, "pubmed:32066987", null, "Zfish OPCs", "GSM3851760", null, "source name:oligodendrocyte precursor cells|transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "Zfish OPCs", "Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013. The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high output flow cell with 50 bp single read  clustered on a cBot with V4 kit. Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells. Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes. The R object .rds  consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log normalized individually with a scale of factor of 10 000. The shared nearest neighbor SNN graph was constructed on cell to cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving SLM algorithm to obtain cell clusters  and visualized with t distributed stochastic neighbor embedding t SNE. The object includes in reductions  tsne  and metadata  Celltype  the embedding and clustering used in the study. Genome build: GRCz11 Supplementary files format and content: Final expression data matrix with 310 cells as used in the study  where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix  where columns belong to celltype and rows to cells. R object .rds.", "oligodendrocyte precursor cells", "no treatment", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "Tgolig1:memYFP zebrafish were raised until  5 dpf", "transgenic line:Tgolig1:memEYFP|tissue:EYFP cells FACS sorted from dissociated whole animal|cell type:oligodendrocyte precursor cells|age:5 dpf", "GSM3851760", "GSM3851760: Zfish OPCs; Danio rerio; RNA Seq", "GSM3851760", null, "1", "A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37\u00b0C  followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP pos/ Propidium Iodite neg; 2. EYFP pos/ Vybrant DyeCycle Ruby pos. SmartSeq2 raw data was processed according to procedures described in S. Picelli et al.  Smart seq2 for sensitive full length transcriptome profiling in single cells. Nat Methods 10  1096 1098 2013", "GEO Accession:GSM3851760", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP200391", null, null, "G18_R1.fastq.gz", "fastq", 35653149.0, 829143.0, "GSM3851760 r153", "0:43", "A:10361320;C:7196014;G:7423127;T:10672688;N:0", 43, null, null, null, 10361320, 7196014, 7423127, 10672688, 0, "SRX5970646", "SRS4876620", "SRA893907", "GEO", "Molecular Neurobiology, MBB, Karolinska Institutet", 1, 0.74257, null, 0.41459, null, 0.92295, null, 0.49361, null, 43, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2019-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 481, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "smartseq", "p2": "Whole Organism"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 453, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 481, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?technology=smartseq&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "cDNA", "label": "cDNA", "count": 416, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_selection=cDNA", "selected": false}, {"value": "RANDOM PCR", "label": "RANDOM PCR", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_selection=RANDOM+PCR", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 31, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_selection=PolyA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 390, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 91, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 481, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "Larval", "label": "Larval", "count": 406, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Larval", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 60, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation_coarse=Juvenile", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "Larval", "label": "Larval", "count": 406, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Larval", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Pharyngula", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Blastula", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Hatching", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Multi-stage", "selected": false}, {"value": "Juvenile", "label": "Juvenile", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Juvenile", "selected": false}, {"value": "Segmentation", "label": "Segmentation", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Segmentation", "selected": false}, {"value": "Zygote", "label": "Zygote", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&devstage_curation=Zygote", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 481, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 481, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism", "results": [{"value": "smartseq", "label": "smartseq", "count": 481, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": "52440", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=smartseq&tissue_curation=Whole+Organism&_next=52440", "private": false, "allow_execute_sql": true, "query_ms": 115.56177199236117}