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481 rows where technology = "smartseq" and tissue_curation = "Whole Organism"

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devstage_curation 8

devstage_curation_coarse 4

experiment.library_selection 3

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 481 ✖

technology 1

  • smartseq · 481 ✖

experiment.platform 1

experiment.library_source 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9775 9775 ERR3838754 ERX3851420 ERS4266444 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma prim5 wt rep2 SAMEA6501995 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501995|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma prim5 wt rep2 p Soma prim5 wt rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 Somatic_prim5_rep2_R1.fastq.gz Somatic_prim5_rep2_R2.fastq.gz fastq fastq 2664555542.0 17942996.0 E MTAB 8707:Somatic prim5 rep2 R 0:74.25 1:74.25 A:757990974;C:568005838;G:586848520;T:749991976;N:1718234 74 74     757990974 568005838 586848520 749991976 1718234 ERX3851420 ERS4266444 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92034 0.91779 0.22669 0.22761 0.74769 0.74911 0.45866 0.45282 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9776 9776 ERR3838753 ERX3851419 ERS4266443 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma prim5 wt rep1 SAMEA6501994 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501994|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma prim5 wt rep1 p Soma prim5 wt rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 Somatic_prim5_rep1_R1.fastq.gz Somatic_prim5_rep1_R2.fastq.gz fastq fastq 1847156504.0 12386853.0 E MTAB 8707:Somatic prim5 rep1 R 0:74.56 1:74.56 A:519724449;C:399975516;G:411702918;T:514818493;N:935128 74 74     519724449 399975516 411702918 514818493 935128 ERX3851419 ERS4266443 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93526 0.93319 0.24244 0.24304 0.75073 0.75201 0.44773 0.44885 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9777 9777 ERR3838752 ERX3851418 ERS4266442 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma prim5 Morpholino rep2 SAMEA6501993 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501993|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma prim5 Morpholino rep2 p Soma prim5 Morpholino rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S14_R1.fastq.gz S14_R2.fastq.gz fastq fastq 953947657.0 6389852.0 E MTAB 8707:S14 R 0:74.64 1:74.65 A:271485260;C:204208876;G:210319402;T:267490986;N:443133 74 74     271485260 204208876 210319402 267490986 443133 ERX3851418 ERS4266442 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93577 0.93619 0.1141 0.11516 0.72644 0.72892 0.4694 0.46965 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9778 9778 ERR3838751 ERX3851417 ERS4266441 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma prim5 Morpholino rep1 SAMEA6501992 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501992|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma prim5 Morpholino rep1 p Soma prim5 Morpholino rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S12_R1.fastq.gz S12_R2.fastq.gz fastq fastq 753719404.0 5057589.0 E MTAB 8707:S12 R 0:74.51 1:74.52 A:216097326;C:160004832;G:164724356;T:212507268;N:385622 74 74     216097326 160004832 164724356 212507268 385622 ERX3851417 ERS4266441 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93958 0.93943 0.10854 0.1092 0.73267 0.73663 0.45629 0.47862 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9779 9779 ERR3838750 ERX3851416 ERS4266440 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma prim5 5mismatch Morpholino rep2 SAMEA6501991 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501991|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma prim5 5mismatch Morpholino rep2 p Soma prim5 5mismatch Morpholino rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S18_R1.fastq.gz S18_R2.fastq.gz fastq fastq 847966718.0 5668126.0 E MTAB 8707:S18 R 0:74.80 1:74.80 A:230723434;C:191446710;G:197114792;T:228326953;N:354829 74 74     230723434 191446710 197114792 228326953 354829 ERX3851416 ERS4266440 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92436 0.92488 0.08973 0.09012 0.73971 0.74192 0.45291 0.45397 76 73 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9780 9780 ERR3838749 ERX3851415 ERS4266439 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma prim5 5mismatch Morpholino rep1 SAMEA6501990 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501990|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma prim5 5mismatch Morpholino rep1 p Soma prim5 5mismatch Morpholino rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S16_R1.fastq.gz S16_R2.fastq.gz fastq fastq 444518989.0 2971315.0 E MTAB 8707:S16 R 0:74.80 1:74.80 A:121398448;C:100282796;G:103112415;T:119559792;N:165538 74 74     121398448 100282796 103112415 119559792 165538 ERX3851415 ERS4266439 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92469 0.92438 0.09917 0.10006 0.72279 0.7251 0.45852 0.46016 73 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9781 9781 ERR3838748 ERX3851414 ERS4266438 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma High rep2 SAMEA6501989 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501989|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep2|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma High rep2 p Soma High rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 Fabio_High_rep2_soma_R1.fastq.gz Fabio_High_rep2_soma_R2.fastq.gz fastq fastq 2072343523.0 13904136.0 E MTAB 8707:Fabio High rep2 soma R 0:74.52 1:74.53 A:596021076;C:439789413;G:451992691;T:583604290;N:936053 74 74     596021076 439789413 451992691 583604290 936053 ERX3851414 ERS4266438 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.94263 0.94098 0.04804 0.04844 0.75797 0.76039 0.50847 0.5014 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9782 9782 ERR3838747 ERX3851413 ERS4266437 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma High rep1 SAMEA6501988 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501988|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma High rep1|age:3.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma High rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma High rep1 p Soma High rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 Somatic_High_rep1_R1.fastq.gz Somatic_High_rep1_R2.fastq.gz fastq fastq 6013555644.0 40662218.0 E MTAB 8707:Somatic High rep1 R 0:73.94 1:73.95 A:1821348300;C:1185534582;G:1227848010;T:1774836657;N:3988095 73 73     1821348300 1185534582 1227848010 1774836657 3988095 ERX3851413 ERS4266437 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93539 0.9357 0.07066 0.07028 0.76197 0.76386 0.54301 0.54343 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9783 9783 ERR3838746 ERX3851412 ERS4266436 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma dome rep2 SAMEA6501987 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501987|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep2|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma dome rep2 p Soma dome rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S10_R1.fastq.gz S10_R2.fastq.gz fastq fastq 1086124503.0 7272505.0 E MTAB 8707:S10 R 0:74.67 1:74.68 A:305920447;C:235855931;G:243442186;T:300439294;N:466645 74 74     305920447 235855931 243442186 300439294 466645 ERX3851412 ERS4266436 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.94089 0.94085 0.04872 0.04916 0.7419 0.74355 0.51209 0.5119 74 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9784 9784 ERR3838745 ERX3851411 ERS4266435 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma dome rep1 SAMEA6501986 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501986|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma dome rep1|age:4.3|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma dome rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma dome rep1 p Soma dome rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S8_R1.fastq.gz S8_R2.fastq.gz fastq fastq 336100162.0 2240589.0 E MTAB 8707:S8 R 0:75.00 1:75.00 A:93960580;C:73499585;G:75981355;T:92580945;N:77697 75 75     93960580 73499585 75981355 92580945 77697 ERX3851411 ERS4266435 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93874 0.93856 0.05265 0.0517 0.74188 0.74381 0.51181 0.51086 75 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9785 9785 ERR3838744 ERX3851410 ERS4266434 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma 256 cell rep2 SAMEA6501985 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501985|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma 256 cell rep2 p Soma 256 cell rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S2_R1.fastq.gz S2_R2.fastq.gz fastq fastq 1272080863.0 8551103.0 E MTAB 8707:S2 R 0:74.38 1:74.38 A:364033393;C:268850689;G:276270908;T:362172455;N:753418 74 74     364033393 268850689 276270908 362172455 753418 ERX3851410 ERS4266434 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.80562 0.80436 0.23702 0.23786 0.77914 0.77991 0.51225 0.5092 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9786 9786 ERR3838743 ERX3851409 ERS4266433 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma 256 cell rep1 SAMEA6501984 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501984|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 256 cell rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma 256 cell rep1 p Soma 256 cell rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 Somatic_256_rep1_R1.fastq.gz Somatic_256_rep1_R2.fastq.gz fastq fastq 2254901578.0 15144857.0 E MTAB 8707:Somatic 256 rep1 R 0:74.44 1:74.45 A:648357135;C:475813294;G:492914743;T:636658631;N:1157775 74 74     648357135 475813294 492914743 636658631 1157775 ERX3851409 ERS4266433 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92992 0.92787 0.07245 0.07214 0.7599 0.76084 0.53758 0.53839 74 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9787 9787 ERR3838742 ERX3851408 ERS4266432 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma 10somites rep2 SAMEA6501983 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501983|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep2|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma 10somites rep2 p Soma 10somites rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S6_R1.fastq.gz S6_R2.fastq.gz fastq fastq 1244080980.0 8338002.0 E MTAB 8707:S6 R 0:74.60 1:74.60 A:356418931;C:263292901;G:270630630;T:353140798;N:597720 74 74     356418931 263292901 270630630 353140798 597720 ERX3851408 ERS4266432 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.86791 0.86732 0.20223 0.20398 0.75588 0.75883 0.4862 0.48313 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
9788 9788 ERR3838741 ERX3851407 ERS4266431 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma 10somites rep1 SAMEA6501982 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501982|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep1|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma 10somites rep1 p Soma 10somites rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S4_R1.fastq.gz S4_R2.fastq.gz fastq fastq 946153328.0 6354843.0 E MTAB 8707:S4 R 0:74.44 1:74.45 A:268310887;C:203457903;G:208969410;T:264875129;N:539999 74 74     268310887 203457903 208969410 264875129 539999 ERX3851407 ERS4266431 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92415 0.92372 0.12138 0.12268 0.74061 0.74422 0.47246 0.47448 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
9789 9789 ERR3838740 ERX3851406 ERS4266430 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC prim5 wt rep2 SAMEA6501981 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501981|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC prim5 wt rep2 p PGC prim5 wt rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 PGC_prim5_rep2_R1.fastq.gz PGC_prim5_rep2_R2.fastq.gz fastq fastq 2236371655.0 15023634.0 E MTAB 8707:PGC prim5 rep2 R 0:74.43 1:74.43 A:619039687;C:495191024;G:509021767;T:611885185;N:1233992 74 74     619039687 495191024 509021767 611885185 1233992 ERX3851406 ERS4266430 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93137 0.92838 0.23991 0.24045 0.71435 0.71591 0.49054 0.49302 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9790 9790 ERR3838739 ERX3851405 ERS4266429 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC prim5 wt rep1 SAMEA6501980 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501980|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC prim5 wt rep1 p PGC prim5 wt rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 PGC_prim5_rep1_R1.fastq.gz PGC_prim5_rep1_R2.fastq.gz fastq fastq 1619398294.0 10873533.0 E MTAB 8707:PGC prim5 rep1 R 0:74.46 1:74.47 A:450612629;C:355178930;G:365650222;T:447083613;N:872900 74 74     450612629 355178930 365650222 447083613 872900 ERX3851405 ERS4266429 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92755 0.92901 0.22893 0.22952 0.71131 0.71372 0.49829 0.50019 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9791 9791 ERR3838738 ERX3851404 ERS4266428 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC prim5 Morpholino rep2 SAMEA6501979 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501979|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC prim5 Morpholino rep2 p PGC prim5 Morpholino rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S13_R1.fastq.gz S13_R2.fastq.gz fastq fastq 906443913.0 6069224.0 E MTAB 8707:S13 R 0:74.67 1:74.68 A:256935983;C:195137600;G:200975999;T:253026767;N:367564 74 74     256935983 195137600 200975999 253026767 367564 ERX3851404 ERS4266428 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93468 0.93605 0.09793 0.09817 0.71163 0.71291 0.48766 0.48921 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9792 9792 ERR3838737 ERX3851403 ERS4266427 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC prim5 Morpholino rep1 SAMEA6501978 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501978|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC prim5 Morpholino rep1 p PGC prim5 Morpholino rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 Fabio_cat_11_R1.fastq.gz Fabio_cat_11_R2.fastq.gz fastq fastq 1078919524.0 7241200.0 E MTAB 8707:Fabio cat 11 R 0:74.50 1:74.50 A:308200726;C:229836659;G:236649504;T:303673221;N:559414 74 74     308200726 229836659 236649504 303673221 559414 ERX3851403 ERS4266427 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93808 0.93753 0.10449 0.10446 0.70733 0.71017 0.48103 0.48247 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9793 9793 ERR3838736 ERX3851402 ERS4266426 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC prim5 5mismatch Morpholino rep2 SAMEA6501977 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501977|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC prim5 5mismatch Morpholino rep2 p PGC prim5 5mismatch Morpholino rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S17_R1.fastq.gz S17_R2.fastq.gz fastq fastq 673911944.0 4501723.0 E MTAB 8707:S17 R 0:74.85 1:74.85 A:184466911;C:150779527;G:155693395;T:182720480;N:251631 74 74     184466911 150779527 155693395 182720480 251631 ERX3851402 ERS4266426 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.9199 0.92023 0.08791 0.08923 0.70132 0.70378 0.49183 0.49425 75 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9794 9794 ERR3838735 ERX3851401 ERS4266425 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC prim5 5mismatch Morpholino rep1 SAMEA6501976 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501976|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC prim5 5mismatch Morpholino rep1 p PGC prim5 5mismatch Morpholino rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S15_R1.fastq.gz S15_R2.fastq.gz fastq fastq 565636692.0 3782000.0 E MTAB 8707:S15 R 0:74.78 1:74.78 A:157353454;C:124504476;G:128260137;T:155314004;N:204621 74 74     157353454 124504476 128260137 155314004 204621 ERX3851401 ERS4266425 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.91956 0.91996 0.08306 0.08458 0.69982 0.70203 0.48525 0.48771 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Pharyngula Embryo Whole Organism All anatomical structures
9795 9795 ERR3838734 ERX3851400 ERS4266424 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC High rep2 SAMEA6501975 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501975|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep2|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC High rep2 p PGC High rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 PGC_High_rep2_R1.fastq.gz PGC_High_rep2_R2.fastq.gz fastq fastq 2491013839.0 16740632.0 E MTAB 8707:PGC High rep2 R 0:74.40 1:74.40 A:715637079;C:527451931;G:545855323;T:700774175;N:1295331 74 74     715637079 527451931 545855323 700774175 1295331 ERX3851400 ERS4266424 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93381 0.93556 0.06095 0.06172 0.76094 0.76364 0.52942 0.53118 74 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9796 9796 ERR3838733 ERX3851399 ERS4266423 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC High rep1 SAMEA6501974 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501974|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC High rep1|age:3.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula high|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC High rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC High rep1 p PGC High rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula high|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 PGC_High_rep1_R1.fastq.gz PGC_High_rep1_R2.fastq.gz fastq fastq 2055218051.0 13801653.0 E MTAB 8707:PGC High rep1 R 0:74.45 1:74.46 A:594747301;C:431446277;G:445665283;T:582330624;N:1028566 74 74     594747301 431446277 445665283 582330624 1028566 ERX3851399 ERS4266423 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93644 0.93494 0.06937 0.07015 0.76353 0.7653 0.45909 0.44979 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9797 9797 ERR3838732 ERX3851398 ERS4266422 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC dome rep2 SAMEA6501973 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501973|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep2|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC dome rep2 p PGC dome rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S9_R1.fastq.gz S9_R2.fastq.gz fastq fastq 882858901.0 5912255.0 E MTAB 8707:S9 R 0:74.66 1:74.67 A:246639630;C:193554406;G:199940889;T:242369366;N:354610 74 74     246639630 193554406 199940889 242369366 354610 ERX3851398 ERS4266422 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.94045 0.9404 0.04635 0.04658 0.74582 0.74777 0.4915 0.49248 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9798 9798 ERR3838731 ERX3851397 ERS4266421 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC dome rep1 SAMEA6501972 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501972|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC dome rep1|age:4.3|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula dome|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC dome rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC dome rep1 p PGC dome rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula dome|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S7_R1.fastq.gz S7_R2.fastq.gz fastq fastq 592299285.0 3961989.0 E MTAB 8707:S7 R 0:74.75 1:74.75 A:166664600;C:128421892;G:132787149;T:164189412;N:236232 74 74     166664600 128421892 132787149 164189412 236232 ERX3851397 ERS4266421 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93981 0.94032 0.04868 0.04843 0.74627 0.74722 0.49243 0.48872 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9799 9799 ERR3838730 ERX3851396 ERS4266420 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 256 cell rep2 SAMEA6501971 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501971|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep2|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC 256 cell rep2 p PGC 256 cell rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S1_R1.fastq.gz S1_R2.fastq.gz fastq fastq 745277323.0 4983607.0 E MTAB 8707:S1 R 0:74.77 1:74.77 A:208352741;C:163024343;G:168234953;T:205391192;N:274094 74 74     208352741 163024343 168234953 205391192 274094 ERX3851396 ERS4266420 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.9393 0.9395 0.03941 0.03941 0.75473 0.75708 0.51338 0.51754 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9800 9800 ERR3838729 ERX3851395 ERS4266419 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 256 cell rep1 SAMEA6501970 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501970|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 256 cell rep1|age:2.5|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:blastula 256 cell|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 256 cell rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC 256 cell rep1 p PGC 256 cell rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:blastula 256 cell|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 PGC_256_rep1_R1.fastq.gz PGC_256_rep1_R2.fastq.gz fastq fastq 1876891175.0 12625794.0 E MTAB 8707:PGC 256 rep1 R 0:74.32 1:74.33 A:539140549;C:396392844;G:411568412;T:528672735;N:1116635 74 74     539140549 396392844 411568412 528672735 1116635 ERX3851395 ERS4266419 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92251 0.92173 0.06705 0.06723 0.76059 0.76374 0.54467 0.54135 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Blastula Embryo Whole Organism All anatomical structures
9801 9801 ERR3838728 ERX3851394 ERS4266418 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 10somites rep2 SAMEA6501969 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501969|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep2|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC 10somites rep2 p PGC 10somites rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S5_R1.fastq.gz S5_R2.fastq.gz fastq fastq 1186993033.0 7958634.0 E MTAB 8707:S5 R 0:74.57 1:74.58 A:332263881;C:259239478;G:267014990;T:327946611;N:528073 74 74     332263881 259239478 267014990 327946611 528073 ERX3851394 ERS4266418 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.90713 0.9062 0.10071 0.1016 0.73058 0.73279 0.48458 0.48038 74 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
9802 9802 ERR3838727 ERX3851393 ERS4266417 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 10somites rep1 SAMEA6501968 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501968|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep1|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC 10somites rep1 p PGC 10somites rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S3_R1.fastq.gz S3_R2.fastq.gz fastq fastq 1230551446.0 8251644.0 E MTAB 8707:S3 R 0:74.56 1:74.57 A:345409587;C:267720436;G:275626594;T:341185818;N:609011 74 74     345409587 267720436 275626594 341185818 609011 ERX3851393 ERS4266417 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.90983 0.90985 0.1005 0.10037 0.72622 0.72825 0.49116 0.49135 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
10111 10111 ERR4911024 ERX4777847 ERS5435613 ERP125516 PRJEB41701 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-9857 Transcriptome Analysis In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC Rescue rep2 SAMEA7678632 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678632|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep2|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 9857:PGC Rescue rep2 p PGC Rescue rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP125516 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09 Tdrd7_Rescue_PGC_rep2_R1.fastq.gz Tdrd7_Rescue_PGC_rep2_R2.fastq.gz fastq fastq 6487121744.0 43103086.0 E MTAB 9857:Tdrd7 Rescue PGC rep2 R 0:75.26 1:75.24 A:1769293880;C:1469053016;G:1516553427;T:1729496045;N:2725376 75 75     1769293880 1469053016 1516553427 1729496045 2725376 ERX4777847 ERS5435613 ERA3184570 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.95185 0.95349 0.04302 0.04315 0.72829 0.73022 0.47176 0.47104 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-12-02 Pharyngula Embryo Whole Organism All anatomical structures
10112 10112 ERR4911023 ERX4777846 ERS5435612 ERP125516 PRJEB41701 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-9857 Transcriptome Analysis In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC Rescue rep1 SAMEA7678631 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678631|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep1|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 9857:PGC Rescue rep1 p PGC Rescue rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP125516 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09 Tdrd7_Rescue_PGC_rep1_R1.fastq.gz Tdrd7_Rescue_PGC_rep1_R2.fastq.gz fastq fastq 5952473889.0 39454929.0 E MTAB 9857:Tdrd7 Rescue PGC rep1 R 0:75.44 1:75.43 A:1640467527;C:1332668425;G:1380033115;T:1597665169;N:1639653 75 75     1640467527 1332668425 1380033115 1597665169 1639653 ERX4777846 ERS5435612 ERA3184570 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.95086 0.95226 0.06292 0.0629 0.70341 0.70579 0.46524 0.46691 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-12-02 Pharyngula Embryo Whole Organism All anatomical structures
10113 10113 ERR4911022 ERX4777845 ERS5435611 ERP125516 PRJEB41701 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-9857 Transcriptome Analysis In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC MO rep2 SAMEA7678630 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678630|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep2|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 9857:PGC MO rep2 p PGC MO rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: compound:tdrd7 targeting MO RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP125516 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09 Tdrd7_MO_PGC_rep2_R1.fastq.gz Tdrd7_MO_PGC_rep2_R2.fastq.gz fastq fastq 906443913.0 6069224.0 E MTAB 9857:Tdrd7 MO PGC rep2 R 0:74.67 1:74.68 A:256935983;C:195137600;G:200975999;T:253026767;N:367564 74 74     256935983 195137600 200975999 253026767 367564 ERX4777845 ERS5435611 ERA3184570 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.93468 0.93603 0.09796 0.09848 0.7119 0.71439 0.48682 0.48933 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-12-02 Pharyngula Embryo Whole Organism All anatomical structures
10114 10114 ERR4911021 ERX4777844 ERS5435610 ERP125516 PRJEB41701 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-9857 Transcriptome Analysis In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC MO rep1 SAMEA7678629 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678629|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep1|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 9857:PGC MO rep1 p PGC MO rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: compound:tdrd7 targeting MO RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP125516 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09 Tdrd7_MO_PGC_rep1_R1.fastq.gz Tdrd7_MO_PGC_rep1_R2.fastq.gz fastq fastq 1078919524.0 7241200.0 E MTAB 9857:Tdrd7 MO PGC rep1 R 0:74.50 1:74.50 A:308200726;C:229836659;G:236649504;T:303673221;N:559414 74 74     308200726 229836659 236649504 303673221 559414 ERX4777844 ERS5435610 ERA3184570 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.938 0.93748 0.10463 0.10431 0.7077 0.70999 0.48098 0.48239 75 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-12-02 Pharyngula Embryo Whole Organism All anatomical structures
10115 10115 ERR4911020 ERX4777843 ERS5435609 ERP125516 PRJEB41701 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-9857 Transcriptome Analysis In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 5mm rep2 SAMEA7678628 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678628|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep2|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 9857:PGC 5mm rep2 p PGC 5mm rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: compound:tdrd7 5mismatch MO RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP125516 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09 Tdrd7_5mm_PGC_rep2_R1.fastq.gz Tdrd7_5mm_PGC_rep2_R2.fastq.gz fastq fastq 673911944.0 4501723.0 E MTAB 9857:Tdrd7 5mm PGC rep2 R 0:74.85 1:74.85 A:184466911;C:150779527;G:155693395;T:182720480;N:251631 74 74     184466911 150779527 155693395 182720480 251631 ERX4777843 ERS5435609 ERA3184570 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.91989 0.92025 0.08795 0.08919 0.70096 0.70416 0.49184 0.49415 75 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-12-02 Pharyngula Embryo Whole Organism All anatomical structures
10116 10116 ERR4911019 ERX4777842 ERS5435608 ERP125516 PRJEB41701 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-9857 Transcriptome Analysis In this rescue experiment embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 5mm rep1 SAMEA7678627 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678627|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep1|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 9857:PGC 5mm rep1 p PGC 5mm rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: compound:tdrd7 5mismatch MO RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP125516 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09 Tdrd7_5mm_PGC_rep1_R1.fastq.gz Tdrd7_5mm_PGC_rep1_R2.fastq.gz fastq fastq 565636692.0 3782000.0 E MTAB 9857:Tdrd7 5mm PGC rep1 R 0:74.78 1:74.78 A:157353454;C:124504476;G:128260137;T:155314004;N:204621 74 74     157353454 124504476 128260137 155314004 204621 ERX4777842 ERS5435608 ERA3184570 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.91957 0.91995 0.08301 0.0845 0.69929 0.70195 0.48544 0.4877 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-12-02 Pharyngula Embryo Whole Organism All anatomical structures
50527 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.   pubmed:30894119   Rneasy unsorted GSM3449971   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   polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina   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   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   SRP167139     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     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   Belgium 2018-10-29 Larval Larval Whole Organism All anatomical structures
50528 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.   pubmed:30894119   RNAqueous unsorted GSM3449970   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   polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology tagmentation and sample barcoding with the Nextera XT kit illumina   cell type:fli:GFP whole embryo|age:5 days|rna isolation kit:RNAqueous micro GSM3449970 GSM3449970: RNAqueous unsorted; Danio rerio; RNA Seq GSM3449970   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   SRP167139     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     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   Belgium 2018-10-29 Larval Larval Whole Organism All anatomical structures
51258 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   pubmed:31451657   total rep 3 GSM3629722   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: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” 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   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   SRP186864     c3.fastq.gz fastq 142798100.0 2855962.0 GSM3629722 r1 0:50 A:33558108;C:34453721;G:38902032;T:35874180;N:10059 50       33558108 34453721 38902032 35874180 10059 SRX5431028 SRS4411023 SRA852308 GEO Department of Biological Sciences, Purdue University 1 0.02673   0.00469   0.98455   0.62342   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq sc single_cell_plate smartseq   United States 2019-02-26 Larval Larval Whole Organism All anatomical structures
51259 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   pubmed:31451657   total rep 2 GSM3629721   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: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” 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   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   SRP186864     c2.fastq.gz fastq 176136650.0 3522733.0 GSM3629721 r1 0:50 A:42179466;C:41890753;G:47676052;T:44377787;N:12592 50       42179466 41890753 47676052 44377787 12592 SRX5431027 SRS4411022 SRA852308 GEO Department of Biological Sciences, Purdue University 1 0.01253   0.00298   0.99342   0.67131   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq sc single_cell_plate smartseq   United States 2019-02-26 Larval Larval Whole Organism All anatomical structures
51260 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   pubmed:31451657   total rep 1 GSM3629720   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: “ alignEndsType EndToEnd outFilterMismatchNmax 1 outFilterMultimapScoreRange 0 outFilterMultimapNmax 10 outSAMunmapped Within outFilterScoreMinOverLread 0 outFilterMatchNminOverLread 0 outFilterMatchNmin 16 alignSJDBoverhangMin 1000” for Samples 6 11: “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” 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   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   SRP186864     c1.fastq.gz fastq 180216500.0 3604330.0 GSM3629720 r1 0:50 A:43005950;C:42787875;G:49009406;T:45400170;N:13099 50       43005950 42787875 49009406 45400170 13099 SRX5431026 SRS4411021 SRA852308 GEO Department of Biological Sciences, Purdue University 1 0.01759   0.00459   0.99101   0.71252   50   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq sc single_cell_plate smartseq   United States 2019-02-26 Larval Larval Whole Organism All anatomical structures
52380 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A10_R1.fastq.gz fastq 22730187.0 528609.0 GSM3851760 r1 0:43 A:6531713;C:4702880;G:4826497;T:6669097;N:0 43       6531713 4702880 4826497 6669097 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86984   0.3317   0.86977   0.50211   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52381 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A19_R1.fastq.gz fastq 25422417.0 591219.0 GSM3851760 r10 0:43 A:7420297;C:5115508;G:5236996;T:7649616;N:0 43       7420297 5115508 5236996 7649616 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85285   0.39693   0.87675   0.44071   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52382 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E13_R1.fastq.gz fastq 34049550.0 791850.0 GSM3851760 r100 0:43 A:9807395;C:7041091;G:7187781;T:10013283;N:0 43       9807395 7041091 7187781 10013283 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86073   0.36367   0.85589   0.48001   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52383 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E14_R1.fastq.gz fastq 30226893.0 702951.0 GSM3851760 r101 0:43 A:8402351;C:6582983;G:6770609;T:8470950;N:0 43       8402351 6582983 6770609 8470950 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87786   0.20548   0.92119   0.5325   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52384 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E15_R1.fastq.gz fastq 31104093.0 723351.0 GSM3851760 r102 0:43 A:8946868;C:6414234;G:6568361;T:9174630;N:0 43       8946868 6414234 6568361 9174630 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85741   0.37503   0.89073   0.48996   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52385 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E16_R1.fastq.gz fastq 34438399.0 800893.0 GSM3851760 r103 0:43 A:9959668;C:7061544;G:7228493;T:10188694;N:0 43       9959668 7061544 7228493 10188694 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85657   0.37381   0.89503   0.47367   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52386 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E17_R1.fastq.gz fastq 31687560.0 736920.0 GSM3851760 r104 0:43 A:9042349;C:6631079;G:6783803;T:9230329;N:0 43       9042349 6631079 6783803 9230329 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86922   0.28531   0.87647   0.50906   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52387 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E18_R1.fastq.gz fastq 28829178.0 670446.0 GSM3851760 r105 0:43 A:8040858;C:6240958;G:6375940;T:8171422;N:0 43       8040858 6240958 6375940 8171422 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.88484   0.25108   0.89796   0.52328   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52388 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E19_R1.fastq.gz fastq 29456161.0 685027.0 GSM3851760 r106 0:43 A:8185810;C:6362322;G:6490611;T:8417418;N:0 43       8185810 6362322 6490611 8417418 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87467   0.2568   0.87637   0.44643   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52389 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E1_R1.fastq.gz fastq 41009788.0 953716.0 GSM3851760 r107 0:43 A:11633133;C:8565119;G:8761780;T:12049756;N:0 43       11633133 8565119 8761780 12049756 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.83802   0.32341   0.88038   0.49748   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52390 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E20_R1.fastq.gz fastq 29314777.0 681739.0 GSM3851760 r108 0:43 A:8470707;C:6002913;G:6136651;T:8704506;N:0 43       8470707 6002913 6136651 8704506 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85476   0.37692   0.87633   0.47456   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52391 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E21_R1.fastq.gz fastq 39374455.0 915685.0 GSM3851760 r109 0:43 A:11315860;C:8119631;G:8323167;T:11615797;N:0 43       11315860 8119631 8323167 11615797 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85391   0.36988   0.91039   0.50229   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52392 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A1_R1.fastq.gz fastq 3574031.0 83117.0 GSM3851760 r11 0:43 A:1037490;C:644669;G:647675;T:1244197;N:0 43       1037490 644669 647675 1244197 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.08124   0.07796   0.99709   0.43644   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52393 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E22_R1.fastq.gz fastq 45159546.0 1050222.0 GSM3851760 r110 0:43 A:13081668;C:9210038;G:9426293;T:13441547;N:0 43       13081668 9210038 9426293 13441547 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.84853   0.41231   0.90678   0.50893   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52394 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E23_R1.fastq.gz fastq 46674522.0 1085454.0 GSM3851760 r111 0:43 A:13407038;C:9644708;G:9870254;T:13752522;N:0 43       13407038 9644708 9870254 13752522 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.8528   0.35087   0.91896   0.50728   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52395 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E24_R1.fastq.gz fastq 40946578.0 952246.0 GSM3851760 r112 0:43 A:11353999;C:8901776;G:9087747;T:11603056;N:0 43       11353999 8901776 9087747 11603056 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.88574   0.2555   0.89203   0.53214   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52396 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E2_R1.fastq.gz fastq 35795909.0 832463.0 GSM3851760 r113 0:43 A:10008515;C:7658565;G:7846504;T:10282325;N:0 43       10008515 7658565 7846504 10282325 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.8507   0.24931   0.87643   0.51656   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52397 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E3_R1.fastq.gz fastq 34867496.0 810872.0 GSM3851760 r114 0:43 A:9952111;C:7269477;G:7461395;T:10184513;N:0 43       9952111 7269477 7461395 10184513 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85806   0.33604   0.85468   0.48609   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52398 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E4_R1.fastq.gz fastq 4629036.0 107652.0 GSM3851760 r115 0:43 A:1294799;C:1008604;G:1044853;T:1280780;N:0 43       1294799 1008604 1044853 1280780 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87228   0.19931   0.94229   0.54841   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52399 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E5_R1.fastq.gz fastq 6320914.0 146998.0 GSM3851760 r116 0:43 A:1861194;C:1147340;G:1160856;T:2151524;N:0 43       1861194 1147340 1160856 2151524 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.0887   0.08394   0.99389   0.4262   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52400 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E6_R1.fastq.gz fastq 32168257.0 748099.0 GSM3851760 r117 0:43 A:9360276;C:6476288;G:6645427;T:9686266;N:0 43       9360276 6476288 6645427 9686266 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.83653   0.4296   0.91171   0.48995   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52401 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E7_R1.fastq.gz fastq 36882089.0 857723.0 GSM3851760 r118 0:43 A:10430067;C:7805495;G:7991940;T:10654587;N:0 43       10430067 7805495 7991940 10654587 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86871   0.29809   0.90011   0.49514   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52402 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E8_R1.fastq.gz fastq 24809839.0 576973.0 GSM3851760 r119 0:43 A:7144307;C:5119783;G:5223795;T:7321954;N:0 43       7144307 5119783 5223795 7321954 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86137   0.37732   0.88611   0.49645   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52403 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A20_R1.fastq.gz fastq 20992729.0 488203.0 GSM3851760 r12 0:43 A:6046890;C:4289153;G:4410467;T:6246219;N:0 43       6046890 4289153 4410467 6246219 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85185   0.31773   0.91845   0.58528   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52404 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     E9_R1.fastq.gz fastq 40215105.0 935235.0 GSM3851760 r120 0:43 A:11360646;C:8521492;G:8730341;T:11602626;N:0 43       11360646 8521492 8730341 11602626 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86307   0.33177   0.8982   0.47644   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52405 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F10_R1.fastq.gz fastq 19107093.0 444351.0 GSM3851760 r121 0:43 A:5563356;C:3848064;G:3951297;T:5744376;N:0 43       5563356 3848064 3951297 5744376 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.84285   0.40366   0.89171   0.48828   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52406 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F11_R1.fastq.gz fastq 31628951.0 735557.0 GSM3851760 r122 0:43 A:9033354;C:6606929;G:6787882;T:9200786;N:0 43       9033354 6606929 6787882 9200786 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86464   0.31248   0.90104   0.50525   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52407 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F12_R1.fastq.gz fastq 24055834.0 559438.0 GSM3851760 r123 0:43 A:6622600;C:5260253;G:5395038;T:6777943;N:0 43       6622600 5260253 5395038 6777943 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87692   0.2118   0.91238   0.42713   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52408 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F13_R1.fastq.gz fastq 27688517.0 643919.0 GSM3851760 r124 0:43 A:8080865;C:5560695;G:5700222;T:8346735;N:0 43       8080865 5560695 5700222 8346735 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.83469   0.43252   0.90938   0.48723   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52409 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F14_R1.fastq.gz fastq 21924754.0 509878.0 GSM3851760 r125 0:43 A:6090527;C:4750408;G:4851102;T:6232717;N:0 43       6090527 4750408 4851102 6232717 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.88707   0.24693   0.89098   0.42985   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52410 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F15_R1.fastq.gz fastq 24524190.0 570330.0 GSM3851760 r126 0:43 A:7099978;C:5008036;G:5144163;T:7272013;N:0 43       7099978 5008036 5144163 7272013 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.84943   0.37319   0.88542   0.49363   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52411 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F16_R1.fastq.gz fastq 22940113.0 533491.0 GSM3851760 r127 0:43 A:6806189;C:4493084;G:4602856;T:7037984;N:0 43       6806189 4493084 4602856 7037984 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.83481   0.50302   0.90155   0.55502   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52412 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F17_R1.fastq.gz fastq 14327600.0 333200.0 GSM3851760 r128 0:43 A:4094254;C:2985444;G:3065124;T:4182778;N:0 43       4094254 2985444 3065124 4182778 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86023   0.27478   0.9262   0.50627   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52413 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F18_R1.fastq.gz fastq 13237507.0 307849.0 GSM3851760 r129 0:43 A:3843212;C:2694145;G:2779980;T:3920170;N:0 43       3843212 2694145 2779980 3920170 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.83869   0.33275   0.89802   0.53459   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52414 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A21_R1.fastq.gz fastq 23607215.0 549005.0 GSM3851760 r13 0:43 A:6949976;C:4679980;G:4802349;T:7174910;N:0 43       6949976 4679980 4802349 7174910 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.84434   0.46159   0.89173   0.46625   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52415 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F19_R1.fastq.gz fastq 28189725.0 655575.0 GSM3851760 r130 0:43 A:7998454;C:5905042;G:6043708;T:8242521;N:0 43       7998454 5905042 6043708 8242521 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86503   0.27006   0.89465   0.50557   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52416 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F1_R1.fastq.gz fastq 19684712.0 457784.0 GSM3851760 r131 0:43 A:5427483;C:4337414;G:4521536;T:5398279;N:0 43       5427483 4337414 4521536 5398279 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87052   0.16084   0.90276   0.50242   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52417 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F20_R1.fastq.gz fastq 25811825.0 600275.0 GSM3851760 r132 0:43 A:7620260;C:5037810;G:5184002;T:7969753;N:0 43       7620260 5037810 5184002 7969753 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.81686   0.50881   0.91031   0.52696   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52418 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F21_R1.fastq.gz fastq 31327564.0 728548.0 GSM3851760 r133 0:43 A:8893372;C:6587100;G:6751304;T:9095788;N:0 43       8893372 6587100 6751304 9095788 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87094   0.28476   0.87797   0.5071   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52419 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F22_R1.fastq.gz fastq 25009187.0 581609.0 GSM3851760 r134 0:43 A:6965919;C:5371799;G:5499602;T:7171867;N:0 43       6965919 5371799 5499602 7171867 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87185   0.25342   0.91214   0.56099   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52420 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F23_R1.fastq.gz fastq 32902998.0 765186.0 GSM3851760 r135 0:43 A:9533499;C:6716093;G:6870853;T:9782553;N:0 43       9533499 6716093 6870853 9782553 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85794   0.35536   0.87671   0.50276   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52421 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F24_R1.fastq.gz fastq 31013578.0 721246.0 GSM3851760 r136 0:43 A:9001008;C:6274940;G:6415769;T:9321861;N:0 43       9001008 6274940 6415769 9321861 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.84095   0.36884   0.92234   0.53474   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52422 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F2_R1.fastq.gz fastq 23623125.0 549375.0 GSM3851760 r137 0:43 A:6462921;C:5250054;G:5397862;T:6512288;N:0 43       6462921 5250054 5397862 6512288 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87991   0.23553   0.91173   0.51346   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52423 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F3_R1.fastq.gz fastq 56849268.0 1322076.0 GSM3851760 r138 0:43 A:15634028;C:12520216;G:12867754;T:15827270;N:0 43       15634028 12520216 12867754 15827270 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.871   0.20701   0.92703   0.49491   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52424 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F4_R1.fastq.gz fastq 46322653.0 1077271.0 GSM3851760 r139 0:43 A:13343135;C:9581671;G:9823311;T:13574536;N:0 43       13343135 9581671 9823311 13574536 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85062   0.40373   0.91281   0.50706   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52425 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A22_R1.fastq.gz fastq 25134059.0 584513.0 GSM3851760 r14 0:43 A:6909921;C:5512326;G:5635533;T:7076279;N:0 43       6909921 5512326 5635533 7076279 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.89127   0.19785   0.90179   0.50794   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52426 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F5_R1.fastq.gz fastq 51033561.0 1186827.0 GSM3851760 r140 0:43 A:14605293;C:10643260;G:10917516;T:14867492;N:0 43       14605293 10643260 10917516 14867492 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85584   0.39713   0.90043   0.48754   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52427 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F6_R1.fastq.gz fastq 11300916.0 262812.0 GSM3851760 r141 0:43 A:3321000;C:2297183;G:2385833;T:3296900;N:0 43       3321000 2297183 2385833 3296900 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.85718   0.4262   0.91914   0.50468   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52428 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F7_R1.fastq.gz fastq 45278742.0 1052994.0 GSM3851760 r142 0:43 A:13002638;C:9369548;G:9622447;T:13284109;N:0 43       13002638 9369548 9622447 13284109 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.83814   0.37647   0.90554   0.49616   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52429 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F8_R1.fastq.gz fastq 14835344.0 345008.0 GSM3851760 r143 0:43 A:4110076;C:3245754;G:3325157;T:4154357;N:0 43       4110076 3245754 3325157 4154357 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86906   0.19318   0.89394   0.51872   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52430 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     F9_R1.fastq.gz fastq 22851017.0 531419.0 GSM3851760 r144 0:43 A:6468358;C:4849150;G:4966680;T:6566829;N:0 43       6468358 4849150 4966680 6566829 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.8823   0.18338   0.88168   0.4915   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52431 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G10_R1.fastq.gz fastq 10655400.0 247800.0 GSM3851760 r145 0:43 A:2964578;C:2045554;G:1988943;T:3656325;N:0 43       2964578 2045554 1988943 3656325 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.08282   0.07443   0.99553   0.77115   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52432 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G11_R1.fastq.gz fastq 38720210.0 900470.0 GSM3851760 r146 0:43 A:10652326;C:8557186;G:8758762;T:10751936;N:0 43       10652326 8557186 8758762 10751936 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87521   0.21283   0.93779   0.50587   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52433 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G12_R1.fastq.gz fastq 37872809.0 880763.0 GSM3851760 r147 0:43 A:10570260;C:8249277;G:8452653;T:10600619;N:0 43       10570260 8249277 8452653 10600619 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.88166   0.24488   0.87265   0.47744   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52434 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G13_R1.fastq.gz fastq 46220313.0 1074891.0 GSM3851760 r148 0:43 A:12943521;C:9974404;G:10197868;T:13104520;N:0 43       12943521 9974404 10197868 13104520 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.86369   0.28235   0.90995   0.5024   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52435 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G14_R1.fastq.gz fastq 22452579.0 522153.0 GSM3851760 r149 0:43 A:6052976;C:5108508;G:5238826;T:6052269;N:0 43       6052976 5108508 5238826 6052269 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.89425   0.12262   0.91234   0.51154   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52436 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     A23_R1.fastq.gz fastq 11064115.0 257305.0 GSM3851760 r15 0:43 A:3312117;C:2015333;G:2092587;T:3644078;N:0 43       3312117 2015333 2092587 3644078 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.67131   0.56353   0.94596   0.46246   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52437 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G15_R1.fastq.gz fastq 26636608.0 619456.0 GSM3851760 r150 0:43 A:7482453;C:5765357;G:5930514;T:7458284;N:0 43       7482453 5765357 5930514 7458284 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.88297   0.26878   0.85979   0.47992   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52438 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G16_R1.fastq.gz fastq 38014150.0 884050.0 GSM3851760 r151 0:43 A:10576888;C:8304761;G:8506878;T:10625623;N:0 43       10576888 8304761 8506878 10625623 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.87683   0.25851   0.89767   0.48845   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52439 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G17_R1.fastq.gz fastq 40972507.0 952849.0 GSM3851760 r152 0:43 A:11958245;C:8186722;G:8404224;T:12423316;N:0 43       11958245 8186722 8404224 12423316 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.79842   0.48846   0.93277   0.51012   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures
52440 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   pubmed:32066987   Zfish OPCs GSM3851760   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°C 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   1 A single cell suspension was generated by incubation of the whole embryo in papain 30min @ 37°C 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   SRP200391     G18_R1.fastq.gz fastq 35653149.0 829143.0 GSM3851760 r153 0:43 A:10361320;C:7196014;G:7423127;T:10672688;N:0 43       10361320 7196014 7423127 10672688 0 SRX5970646 SRS4876620 SRA893907 GEO Molecular Neurobiology, MBB, Karolinska Institutet 1 0.74257   0.41459   0.92295   0.49361   43   B   usable mapping rate illumina hiseq_era full_length random_priming unknown sc single_cell_plate smartseq   Sweden 2019-06-04 Larval Larval Whole Organism All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;