rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
9775,ERR3838754,ERX3851420,ERS4266444,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 wt rep2,SAMEA6501995,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501995|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 wt rep2 p,Soma prim5 wt rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_prim5_rep2_R1.fastq.gz Somatic_prim5_rep2_R2.fastq.gz,fastq fastq,2664555542.0,17942996.0,E MTAB 8707:Somatic prim5 rep2 R,0:74.25 1:74.25,A:757990974;C:568005838;G:586848520;T:749991976;N:1718234,74,74,,,757990974,568005838,586848520,749991976,1718234,ERX3851420,ERS4266444,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92034,0.91779,0.22669,0.22761,0.74769,0.74911,0.45866,0.45282,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9776,ERR3838753,ERX3851419,ERS4266443,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 wt rep1,SAMEA6501994,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501994|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 wt rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 wt rep1 p,Soma prim5 wt rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Somatic_prim5_rep1_R1.fastq.gz Somatic_prim5_rep1_R2.fastq.gz,fastq fastq,1847156504.0,12386853.0,E MTAB 8707:Somatic prim5 rep1 R,0:74.56 1:74.56,A:519724449;C:399975516;G:411702918;T:514818493;N:935128,74,74,,,519724449,399975516,411702918,514818493,935128,ERX3851419,ERS4266443,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93526,0.93319,0.24244,0.24304,0.75073,0.75201,0.44773,0.44885,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9777,ERR3838752,ERX3851418,ERS4266442,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 Morpholino rep2,SAMEA6501993,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501993|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 Morpholino rep2 p,Soma prim5 Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S14_R1.fastq.gz S14_R2.fastq.gz,fastq fastq,953947657.0,6389852.0,E MTAB 8707:S14 R,0:74.64 1:74.65,A:271485260;C:204208876;G:210319402;T:267490986;N:443133,74,74,,,271485260,204208876,210319402,267490986,443133,ERX3851418,ERS4266442,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93577,0.93619,0.1141,0.11516,0.72644,0.72892,0.4694,0.46965,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9778,ERR3838751,ERX3851417,ERS4266441,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 Morpholino rep1,SAMEA6501992,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501992|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 Morpholino rep1 p,Soma prim5 Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S12_R1.fastq.gz S12_R2.fastq.gz,fastq fastq,753719404.0,5057589.0,E MTAB 8707:S12 R,0:74.51 1:74.52,A:216097326;C:160004832;G:164724356;T:212507268;N:385622,74,74,,,216097326,160004832,164724356,212507268,385622,ERX3851417,ERS4266441,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93958,0.93943,0.10854,0.1092,0.73267,0.73663,0.45629,0.47862,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9779,ERR3838750,ERX3851416,ERS4266440,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 5mismatch Morpholino rep2,SAMEA6501991,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501991|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 5mismatch Morpholino rep2 p,Soma prim5 5mismatch Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S18_R1.fastq.gz S18_R2.fastq.gz,fastq fastq,847966718.0,5668126.0,E MTAB 8707:S18 R,0:74.80 1:74.80,A:230723434;C:191446710;G:197114792;T:228326953;N:354829,74,74,,,230723434,191446710,197114792,228326953,354829,ERX3851416,ERS4266440,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92436,0.92488,0.08973,0.09012,0.73971,0.74192,0.45291,0.45397,76,73,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9780,ERR3838749,ERX3851415,ERS4266439,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Soma prim5 5mismatch Morpholino rep1,SAMEA6501990,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:01Z|External Id:SAMEA6501990|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:01Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:Soma prim5 5mismatch Morpholino rep1 p,Soma prim5 5mismatch Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:whole embryo,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S16_R1.fastq.gz S16_R2.fastq.gz,fastq fastq,444518989.0,2971315.0,E MTAB 8707:S16 R,0:74.80 1:74.80,A:121398448;C:100282796;G:103112415;T:119559792;N:165538,74,74,,,121398448,100282796,103112415,119559792,165538,ERX3851415,ERS4266439,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92469,0.92438,0.09917,0.10006,0.72279,0.7251,0.45852,0.46016,73,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9789,ERR3838740,ERX3851406,ERS4266430,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 wt rep2,SAMEA6501981,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501981|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 wt rep2 p,PGC prim5 wt rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_prim5_rep2_R1.fastq.gz PGC_prim5_rep2_R2.fastq.gz,fastq fastq,2236371655.0,15023634.0,E MTAB 8707:PGC prim5 rep2 R,0:74.43 1:74.43,A:619039687;C:495191024;G:509021767;T:611885185;N:1233992,74,74,,,619039687,495191024,509021767,611885185,1233992,ERX3851406,ERS4266430,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93137,0.92838,0.23991,0.24045,0.71435,0.71591,0.49054,0.49302,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9790,ERR3838739,ERX3851405,ERS4266429,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 wt rep1,SAMEA6501980,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501980|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 wt rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 wt rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 wt rep1 p,PGC prim5 wt rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,PGC_prim5_rep1_R1.fastq.gz PGC_prim5_rep1_R2.fastq.gz,fastq fastq,1619398294.0,10873533.0,E MTAB 8707:PGC prim5 rep1 R,0:74.46 1:74.47,A:450612629;C:355178930;G:365650222;T:447083613;N:872900,74,74,,,450612629,355178930,365650222,447083613,872900,ERX3851405,ERS4266429,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.92755,0.92901,0.22893,0.22952,0.71131,0.71372,0.49829,0.50019,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9791,ERR3838738,ERX3851404,ERS4266428,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 Morpholino rep2,SAMEA6501979,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501979|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 Morpholino rep2 p,PGC prim5 Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S13_R1.fastq.gz S13_R2.fastq.gz,fastq fastq,906443913.0,6069224.0,E MTAB 8707:S13 R,0:74.67 1:74.68,A:256935983;C:195137600;G:200975999;T:253026767;N:367564,74,74,,,256935983,195137600,200975999,253026767,367564,ERX3851404,ERS4266428,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93468,0.93605,0.09793,0.09817,0.71163,0.71291,0.48766,0.48921,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9792,ERR3838737,ERX3851403,ERS4266427,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 Morpholino rep1,SAMEA6501978,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501978|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 Morpholino rep1 p,PGC prim5 Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Morpholino antisense oligo against Tdrd7 transcript|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,Fabio_cat_11_R1.fastq.gz Fabio_cat_11_R2.fastq.gz,fastq fastq,1078919524.0,7241200.0,E MTAB 8707:Fabio cat 11 R,0:74.50 1:74.50,A:308200726;C:229836659;G:236649504;T:303673221;N:559414,74,74,,,308200726,229836659,236649504,303673221,559414,ERX3851403,ERS4266427,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93808,0.93753,0.10449,0.10446,0.70733,0.71017,0.48103,0.48247,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9793,ERR3838736,ERX3851402,ERS4266426,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 5mismatch Morpholino rep2,SAMEA6501977,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501977|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 5mismatch Morpholino rep2 p,PGC prim5 5mismatch Morpholino rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S17_R1.fastq.gz S17_R2.fastq.gz,fastq fastq,673911944.0,4501723.0,E MTAB 8707:S17 R,0:74.85 1:74.85,A:184466911;C:150779527;G:155693395;T:182720480;N:251631,74,74,,,184466911,150779527,155693395,182720480,251631,ERX3851402,ERS4266426,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.9199,0.92023,0.08791,0.08923,0.70132,0.70378,0.49183,0.49425,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
9794,ERR3838735,ERX3851401,ERS4266425,ERP119601,PRJEB36411,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-8707,Transcriptome Analysis,Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell  high  dome  10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC prim5 5mismatch Morpholino rep1,SAMEA6501976,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501976|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC prim5 5mismatch Morpholino rep1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 8707:PGC prim5 5mismatch Morpholino rep1 p,PGC prim5 5mismatch Morpholino rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: compound:Control morpholino antisense oligo with 5 mismatches|Experimental Factor: dose:0.3|Experimental Factor: cell type:primordial germ cell,OTHER,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP119601,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24,S15_R1.fastq.gz S15_R2.fastq.gz,fastq fastq,565636692.0,3782000.0,E MTAB 8707:S15 R,0:74.78 1:74.78,A:157353454;C:124504476;G:128260137;T:155314004;N:204621,74,74,,,157353454,124504476,128260137,155314004,204621,ERX3851401,ERS4266425,ERA2354529,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.91956,0.91996,0.08306,0.08458,0.69982,0.70203,0.48525,0.48771,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-01-24,Pharyngula,Embryo,Whole Organism,All anatomical structures
10111,ERR4911024,ERX4777847,ERS5435613,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC Rescue rep2,SAMEA7678632,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678632|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep2|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC Rescue rep2 p,PGC Rescue rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_Rescue_PGC_rep2_R1.fastq.gz Tdrd7_Rescue_PGC_rep2_R2.fastq.gz,fastq fastq,6487121744.0,43103086.0,E MTAB 9857:Tdrd7 Rescue PGC rep2 R,0:75.26 1:75.24,A:1769293880;C:1469053016;G:1516553427;T:1729496045;N:2725376,75,75,,,1769293880,1469053016,1516553427,1729496045,2725376,ERX4777847,ERS5435613,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.95185,0.95349,0.04302,0.04315,0.72829,0.73022,0.47176,0.47104,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10112,ERR4911023,ERX4777846,ERS5435612,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC Rescue rep1,SAMEA7678631,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678631|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC Rescue rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC Rescue rep1|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC Rescue rep1 p,PGC Rescue rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 MO + tdrd7 rescue RNA,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_Rescue_PGC_rep1_R1.fastq.gz Tdrd7_Rescue_PGC_rep1_R2.fastq.gz,fastq fastq,5952473889.0,39454929.0,E MTAB 9857:Tdrd7 Rescue PGC rep1 R,0:75.44 1:75.43,A:1640467527;C:1332668425;G:1380033115;T:1597665169;N:1639653,75,75,,,1640467527,1332668425,1380033115,1597665169,1639653,ERX4777846,ERS5435612,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.95086,0.95226,0.06292,0.0629,0.70341,0.70579,0.46524,0.46691,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10113,ERR4911022,ERX4777845,ERS5435611,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC MO rep2,SAMEA7678630,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678630|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep2|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC MO rep2 p,PGC MO rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 targeting MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_MO_PGC_rep2_R1.fastq.gz Tdrd7_MO_PGC_rep2_R2.fastq.gz,fastq fastq,906443913.0,6069224.0,E MTAB 9857:Tdrd7 MO PGC rep2 R,0:74.67 1:74.68,A:256935983;C:195137600;G:200975999;T:253026767;N:367564,74,74,,,256935983,195137600,200975999,253026767,367564,ERX4777845,ERS5435611,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.93468,0.93603,0.09796,0.09848,0.7119,0.71439,0.48682,0.48933,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10114,ERR4911021,ERX4777844,ERS5435610,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC MO rep1,SAMEA7678629,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678629|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC MO rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC MO rep1|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC MO rep1 p,PGC MO rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 targeting MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_MO_PGC_rep1_R1.fastq.gz Tdrd7_MO_PGC_rep1_R2.fastq.gz,fastq fastq,1078919524.0,7241200.0,E MTAB 9857:Tdrd7 MO PGC rep1 R,0:74.50 1:74.50,A:308200726;C:229836659;G:236649504;T:303673221;N:559414,74,74,,,308200726,229836659,236649504,303673221,559414,ERX4777844,ERS5435610,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.938,0.93748,0.10463,0.10431,0.7077,0.70999,0.48098,0.48239,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10115,ERR4911020,ERX4777843,ERS5435609,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 5mm rep2,SAMEA7678628,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678628|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep2|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep2|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC 5mm rep2 p,PGC 5mm rep2 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 5mismatch MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_5mm_PGC_rep2_R1.fastq.gz Tdrd7_5mm_PGC_rep2_R2.fastq.gz,fastq fastq,673911944.0,4501723.0,E MTAB 9857:Tdrd7 5mm PGC rep2 R,0:74.85 1:74.85,A:184466911;C:150779527;G:155693395;T:182720480;N:251631,74,74,,,184466911,150779527,155693395,182720480,251631,ERX4777843,ERS5435609,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.91989,0.92025,0.08795,0.08919,0.70096,0.70416,0.49184,0.49415,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
10116,ERR4911019,ERX4777842,ERS5435608,ERP125516,PRJEB41701,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E-MTAB-9857,Transcriptome Analysis,In this rescue experiment  embryos were injected with a Tdrd7 targeting morpholino to block translation of tdrd7 RNA and simultaneously provided with a Tdrd7 morpholino resistant RNA.,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 02,,Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,PGC 5mm rep1,SAMEA7678627,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK",ENA first public:2020 12 24|ENA last update:2020 12 02|External Id:SAMEA7678627|INSDC center alias:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine  Imperial College  London  UK|INSDC first public:2020 12 24T04:05:28Z|INSDC last update:2020 12 02T17:13:26Z|INSDC status:public|Submitter Id:E MTAB 9857:PGC 5mm rep1|age:24|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:pharyngula prim 5|genotype:tgbuc:gfp|sample name:E MTAB 9857:PGC 5mm rep1|strain:AB,,,,,,,,,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,E MTAB 9857:PGC 5mm rep1 p,PGC 5mm rep1 p,RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Morpholino antisense oligos were used in order to inhibit Tdrd7 translation during zebrafish development. Stock morpholinos were diluted in phenol red and about 0.3 pM were injected into the yolk of a fertilised zebrafish embryo. As experimental control  a group of embryos were injected with morpholinos having 5 mismatches for the target Tdrd7 transcript. A rescue experiment was performed with Tdrd7 MO resistant RNA from tdrd7 transcript. The RNA was in vitro transcribed and co injected in once cell embryo to rescue MO mediated Tdrd7 KD.   Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit  as from manufacturer's instruction. In brief  reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe  634889  France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter  A63880  USA.,Experimental Factor: compound:tdrd7 5mismatch MO,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,NextSeq 550,,ERP125516,NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis,ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 12 09,Tdrd7_5mm_PGC_rep1_R1.fastq.gz Tdrd7_5mm_PGC_rep1_R2.fastq.gz,fastq fastq,565636692.0,3782000.0,E MTAB 9857:Tdrd7 5mm PGC rep1 R,0:74.78 1:74.78,A:157353454;C:124504476;G:128260137;T:155314004;N:204621,74,74,,,157353454,124504476,128260137,155314004,204621,ERX4777842,ERS5435608,ERA3184570,"MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive","MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive",2,0.91957,0.91995,0.08301,0.0845,0.69929,0.70195,0.48544,0.4877,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,United Kingdom,2020-12-02,Pharyngula,Embryo,Whole Organism,All anatomical structures
19098,ERR13822110,ERX13224862,ERS21098697,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR2 S2 R1 001.fastq.gz,38 PR2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR2,webin reads 38 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR2_S2_R1_001.fastq.gz,fastq,3463281109.0,34821985.0,webin reads 38 PR2,0:99.46,A:969862466;C:733798241;G:755135957;T:1004440555;N:43890,99,,,,969862466,733798241,755135957,1004440555,43890,ERX13224862,ERS21098697,ERA30879238,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19099,ERR13822784,ERX13225536,ERS21098706,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC3 S11 R1 001.fastq.gz,38 HC3,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC3,webin reads 38 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC3_S11_R1_001.fastq.gz,fastq,4360921873.0,44107486.0,webin reads 38 HC3,0:98.87,A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882,98,,,,1222778761,918257887,948838973,1270939370,106882,ERX13225536,ERS21098706,ERA30879613,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19103,ERR13822197,ERX13224949,ERS21098704,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC1 S9 R1 001.fastq.gz,SAMEA116100624,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 HC1,webin reads 38 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC1_S9_R1_001.fastq.gz,fastq,3784641498.0,38331162.0,webin reads 38 HC1,0:98.74,A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167,98,,,,1064199311,791310791,818910597,1110118632,102167,ERX13224949,ERS21098704,ERA30879548,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19106,ERR13822131,ERX13224883,ERS21098700,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC1 S5 R1 001.fastq.gz,SAMEA116100620,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 AC1,webin reads 38 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC1_S5_R1_001.fastq.gz,fastq,3836921113.0,38702139.0,webin reads 38 AC1,0:99.14,A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693,99,,,,1066720805,818958589,843762182,1107403844,75693,ERX13224883,ERS21098700,ERA30879356,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19107,ERR13822143,ERX13224895,ERS21098702,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC3 S7 R1 001.fastq.gz,38 AC3,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC3,webin reads 38 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC3_S7_R1_001.fastq.gz,fastq,3452707377.0,34902410.0,webin reads 38 AC3,0:98.92,A:970868997;C:726795179;G:750560378;T:1004408693;N:74130,98,,,,970868997,726795179,750560378,1004408693,74130,ERX13224895,ERS21098702,ERA30879451,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19109,ERR13822153,ERX13224905,ERS21098703,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC4 S8 R1 001.fastq.gz,38 AC4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC4,webin reads 38 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC4_S8_R1_001.fastq.gz,fastq,4130629624.0,41794865.0,webin reads 38 AC4,0:98.83,A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277,98,,,,1156746387,877063962,905379690,1191264308,175277,ERX13224905,ERS21098703,ERA30879532,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19110,ERR13822201,ERX13224953,ERS21098705,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC2 S10 R1 001.fastq.gz,38 HC2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC2,webin reads 38 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC2_S10_R1_001.fastq.gz,fastq,4221340137.0,42584743.0,webin reads 38 HC2,0:99.13,A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761,99,,,,1195817135,879958039,908085464,1237394738,84761,ERX13224953,ERS21098705,ERA30879582,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19111,ERR13822114,ERX13224866,ERS21098698,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR3 S3 R1 001.fastq.gz,SAMEA116100618,GIMM,ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina,,,,,,,,,Raw reads: 38 PR3,webin reads 38 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR3_S3_R1_001.fastq.gz,fastq,3894010106.0,39196855.0,webin reads 38 PR3,0:99.34,A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488,99,,,,1093221995,818047738,843661747,1138957138,121488,ERX13224866,ERS21098698,ERA30879273,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2024-01-01,Pharyngula,Embryo,Eye,Sensory System
19112,ERR13822135,ERX13224887,ERS21098701,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38AC2 S6 R1 001.fastq.gz,38 AC2,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 AC2,webin reads 38 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 AC2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38AC2_S6_R1_001.fastq.gz,fastq,3913343007.0,39682834.0,webin reads 38 AC2,0:98.62,A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960,98,,,,1089960083,827936673,855955684,1139372607,117960,ERX13224887,ERS21098701,ERA30879382,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19115,ERR13822099,ERX13224851,ERS21098696,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR1 S1 R1 001.fastq.gz,38 PR1,,organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR1,webin reads 38 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR1,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR1_S1_R1_001.fastq.gz,fastq,4256158288.0,42658127.0,webin reads 38 PR1,0:99.77,A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845,99,,,,1193880575,899261652,926114030,1236860186,41845,ERX13224851,ERS21098696,ERA30879152,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19116,ERR13822119,ERX13224871,ERS21098699,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38PR4 S4 R1 001.fastq.gz,38 PR4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 PR4,webin reads 38 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 PR4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38PR4_S4_R1_001.fastq.gz,fastq,3726308046.0,37591038.0,webin reads 38 PR4,0:99.13,A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180,99,,,,1043231302,789255840,812957881,1080801843,61180,ERX13224871,ERS21098699,ERA30879302,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
19120,ERR13822788,ERX13225540,ERS21098707,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,38HC4 S12 R1 001.fastq.gz,38 HC4,,organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal,,,,,,,,,Raw reads: 38 HC4,webin reads 38 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 38 HC4,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,38HC4_S12_R1_001.fastq.gz,fastq,3353994440.0,33744828.0,webin reads 38 HC4,0:99.39,A:939537209;C:709367668;G:731849729;T:973193819;N:46015,99,,,,939537209,709367668,731849729,973193819,46015,ERX13225540,ERS21098707,ERA30879650,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Pharyngula,Embryo,Eye,Sensory System
25091,SRR25567703,SRX21296461,SRS18545739,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696246,GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696246 r1,GSM7696246,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,413-Tie1-KO2_S4_L001_R1_001.fastq.gz,fastq,445428400.0,5860900.0,GSM7696246 r1,0:76,A:143568074;C:79903177;G:79677344;T:142230186;N:49619,76,,,,143568074,79903177,79677344,142230186,49619,SRX21296461,SRS18545739,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.75644,,0.67481,,0.78062,,0.49002,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25092,SRR25567704,SRX21296461,SRS18545739,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696246,GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696246 r1,GSM7696246,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,413-Tie1-KO2_S4_L002_R1_001.fastq.gz,fastq,436280280.0,5740530.0,GSM7696246 r2,0:76,A:140668025;C:78248456;G:77919880;T:139381210;N:62709,76,,,,140668025,78248456,77919880,139381210,62709,SRX21296461,SRS18545739,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.75737,,0.67543,,0.77796,,0.494,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25093,SRR25567705,SRX21296461,SRS18545739,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696246,GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696246 r1,GSM7696246,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,413-Tie1-KO2_S4_L003_R1_001.fastq.gz,fastq,453115800.0,5962050.0,GSM7696246 r3,0:76,A:145977328;C:81331359;G:81042932;T:144726596;N:37585,76,,,,145977328,81331359,81042932,144726596,37585,SRX21296461,SRS18545739,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.75941,,0.67812,,0.78255,,0.49198,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25094,SRR25567706,SRX21296461,SRS18545739,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 2  RNAseq,GSM7696246,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696246,GSM7696246: EC  tie1 Homo  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696246 r1,GSM7696246,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,413-Tie1-KO2_S4_L004_R1_001.fastq.gz,fastq,451629316.0,5942491.0,GSM7696246 r4,0:76,A:145539227;C:81081378;G:80692220;T:144283694;N:32797,76,,,,145539227,81081378,80692220,144283694,32797,SRX21296461,SRS18545739,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.75907,,0.67763,,0.78074,,0.49757,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25095,SRR25567707,SRX21296460,SRS18545738,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696245,GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696245 r1,GSM7696245,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,412-Tie1-KO1_S3_L001_R1_001.fastq.gz,fastq,438903344.0,5775044.0,GSM7696245 r1,0:76,A:141636851;C:79318996;G:78779375;T:139120411;N:47711,76,,,,141636851,79318996,78779375,139120411,47711,SRX21296460,SRS18545738,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.76357,,0.65866,,0.76238,,0.48958,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25096,SRR25567708,SRX21296460,SRS18545738,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696245,GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696245 r1,GSM7696245,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,412-Tie1-KO1_S3_L002_R1_001.fastq.gz,fastq,429344216.0,5649266.0,GSM7696245 r2,0:76,A:138620131;C:77579442;G:76950101;T:136131396;N:63146,76,,,,138620131,77579442,76950101,136131396,63146,SRX21296460,SRS18545738,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.76216,,0.65728,,0.76132,,0.4958,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25097,SRR25567709,SRX21296460,SRS18545738,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696245,GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696245 r1,GSM7696245,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,412-Tie1-KO1_S3_L003_R1_001.fastq.gz,fastq,446301792.0,5872392.0,GSM7696245 r3,0:76,A:143941333;C:80689335;G:80111561;T:141523625;N:35938,76,,,,143941333,80689335,80111561,141523625,35938,SRX21296460,SRS18545738,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.76416,,0.65858,,0.76177,,0.48634,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25098,SRR25567710,SRX21296460,SRS18545738,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 Homo  replicate 1  RNAseq,GSM7696245,,source name:homozygous tie1 mutant embryos|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 Homo  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,homozygous tie1 mutant embryos,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696245,GSM7696245: EC  tie1 Homo  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696245 r1,GSM7696245,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,412-Tie1-KO1_S3_L004_R1_001.fastq.gz,fastq,443971252.0,5841727.0,GSM7696245 r4,0:76,A:143197029;C:80287228;G:79639533;T:140816381;N:31081,76,,,,143197029,80287228,79639533,140816381,31081,SRX21296460,SRS18545738,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.77093,,0.66467,,0.76081,,0.49407,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25099,SRR25567711,SRX21296459,SRS18545737,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696244,GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696244 r1,GSM7696244,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,411-Tie1-WT-HT2_S2_L001_R1_001.fastq.gz,fastq,392537796.0,5164971.0,GSM7696244 r1,0:76,A:124144181;C:72762157;G:72562894;T:123025322;N:43242,76,,,,124144181,72762157,72562894,123025322,43242,SRX21296459,SRS18545737,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.78106,,0.59772,,0.73553,,0.48949,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25100,SRR25567712,SRX21296459,SRS18545737,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696244,GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696244 r1,GSM7696244,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,411-Tie1-WT-HT2_S2_L002_R1_001.fastq.gz,fastq,384487572.0,5059047.0,GSM7696244 r2,0:76,A:121620414;C:71266999;G:70967086;T:120577709;N:55364,76,,,,121620414,71266999,70967086,120577709,55364,SRX21296459,SRS18545737,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.77986,,0.59517,,0.73547,,0.48651,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25101,SRR25567713,SRX21296459,SRS18545737,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696244,GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696244 r1,GSM7696244,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,411-Tie1-WT-HT2_S2_L003_R1_001.fastq.gz,fastq,399939360.0,5262360.0,GSM7696244 r3,0:76,A:126400057;C:74196301;G:73931308;T:125379595;N:32099,76,,,,126400057,74196301,73931308,125379595,32099,SRX21296459,SRS18545737,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.77917,,0.59465,,0.7359,,0.48952,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25102,SRR25567714,SRX21296459,SRS18545737,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 2  RNAseq,GSM7696244,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 2  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696244,GSM7696244: EC  tie1 WT/Het  replicate 2  RNAseq; Danio rerio; RNA Seq,GSM7696244 r1,GSM7696244,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,411-Tie1-WT-HT2_S2_L004_R1_001.fastq.gz,fastq,398035712.0,5237312.0,GSM7696244 r4,0:76,A:125843687;C:73845902;G:73489490;T:124828195;N:28438,76,,,,125843687,73845902,73489490,124828195,28438,SRX21296459,SRS18545737,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.77934,,0.59613,,0.73608,,0.48475,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25103,SRR25567715,SRX21296458,SRS18545736,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696243,GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696243 r1,GSM7696243,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,410-Tie1-WT-HT1_S1_L001_R1_001.fastq.gz,fastq,412291944.0,5424894.0,GSM7696243 r1,0:76,A:129182868;C:77123147;G:77053023;T:128887593;N:45313,76,,,,129182868,77123147,77053023,128887593,45313,SRX21296458,SRS18545736,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.79085,,0.52962,,0.7349,,0.48594,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25104,SRR25567716,SRX21296458,SRS18545736,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696243,GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696243 r1,GSM7696243,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,410-Tie1-WT-HT1_S1_L002_R1_001.fastq.gz,fastq,404294768.0,5319668.0,GSM7696243 r2,0:76,A:126685179;C:75658897;G:75455501;T:126437486;N:57705,76,,,,126685179,75658897,75455501,126437486,57705,SRX21296458,SRS18545736,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.79163,,0.52938,,0.73304,,0.48118,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25105,SRR25567717,SRX21296458,SRS18545736,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696243,GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696243 r1,GSM7696243,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,410-Tie1-WT-HT1_S1_L003_R1_001.fastq.gz,fastq,419693128.0,5522278.0,GSM7696243 r3,0:76,A:131491219;C:78551884;G:78434940;T:131179828;N:35257,76,,,,131491219,78551884,78434940,131179828,35257,SRX21296458,SRS18545736,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.79077,,0.52836,,0.73419,,0.48215,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
25106,SRR25567718,SRX21296458,SRS18545736,SRP453968,PRJNA1003386,Transcriptional profiles of venous and lymphatic endothelial cells from tie1 mutant zebrafish,GSE240329,Transcriptome Analysis,To investigate what kind of gene expression is regulated downstream of Tie1 signaling  we performed RNA seq analyses on venous and lymphatic endothelial cells ECs between homozygous tie1 mutant embryos and their wild type and heterozygous siblings during secondary sprouting  respectively. Our analyses indicate that Tie1 signaling controls a series of gene expression involved in lymphatic development including EC migration  proliferation  and differentiation. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells from homozygous tie1 mutant embryos and their wild type and heterozygous siblings in zebrafish.,,pubmed:38742432,,EC  tie1 WT/Het  replicate 1  RNAseq,GSM7696243,,source name:wild type and heterozygous siblings|tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed|geo loc name:missing|collection date:missing,EC  tie1 WT/Het  replicate 1  RNAseq,RNA Seq data were trimmed using Trim Galore version 0.6.6 and Cutadapt version 2.8. The reads were mapped to a reference genome GRCz11 using HISAT2 version 2.2.1  and the resulting aligned reads were sorted and indexed using SAMtools version 1.7. Relative abundances of genes were measured in TPM using StringTie version 2.1.4. Assembly: GRCz 11 Supplementary files format and content: Excel CSV files include transcripts per million TPM for each sample.,wild type and heterozygous siblings,,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer’s instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,tissue:Trunk and Tail|cell type:Endothelial cells|genotype:Tgkdrl:EGFP;Tglyve1:DsRed,GSM7696243,GSM7696243: EC  tie1 WT/Het  replicate 1  RNAseq; Danio rerio; RNA Seq,GSM7696243 r1,GSM7696243,1,Trunk and tail region from 47 hpf Tgkdrl:EGFP;Tglyve1:DsRed tie1 /  zebrafish embryos with blood flow and their tie1+/? siblings were manually dissected and collected into a low binding 12 well plate. post washed in E3 media  samples were incubated with 1 ml of lysis solution containing collagenase P Roche and TrypLE Express Enzyme Gibco for 20 minutes under occasional pipetting. The dissociated cells in suspension medium phenol red free DMEM with 1% FBS  0.8 mM calcium chloride  50 U/ml penicillin  and 0.05 mg/ml streptomycin were subjected to cell sorting using a FACS Aria III cell sorter BD Bioscience. EGFP and DsRed double positive cells were collected as venous and lymphatic endothelial cells for further RNA preparation. Total RNAs were prepared from kdrl:EGFP+/lyve1:DsRed+ ECs of tie1 /  embryos and their tie1+/? siblings using the NucleoSpin XS kit Macherey Nagel  740902.50 according to the manufacturer's instructions. Reverse transcription and cDNA library preparation were performed with a SMART Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech  634888. Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs  E7760,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP453968,,,410-Tie1-WT-HT1_S1_L004_R1_001.fastq.gz,fastq,418155268.0,5502043.0,GSM7696243 r4,0:76,A:130978746;C:78285682;G:78062725;T:130798846;N:29269,76,,,,130978746,78285682,78062725,130798846,29269,SRX21296458,SRS18545736,SRA1688627,"Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute","Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute",1,0.78728,,0.52541,,0.73484,,0.48813,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,nebnext,sc,single_cell_plate,smartseq,,Japan,2023-08-08,Pharyngula,Embryo,Multi-tissue,Multi-system
34548,SRR32104353,SRX27449957,SRS23876478,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,24hpf TrunkNC 3,GSM8751790,,source name:trunk NC tissue from somite 7 to somite 16|tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+|geo loc name:missing|collection date:missing,24hpf TrunkNC 3,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,trunk NC tissue from somite 7 to somite 16,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+,GSM8751790,GSM8751790: 24hpf TrunkNC 3; Danio rerio; RNA Seq,GSM8751790 r1,GSM8751790,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10+3_Trunk_24h_19733_R1_combined_filtered.fastq.gz,fastq,1792416000.0,35848320.0,GSM8751790 r1,0:50,A:512975947;C:383333260;G:389199848;T:506816777;N:90168,50,,,,512975947,383333260,389199848,506816777,90168,SRX27449957,SRS23876478,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Pharyngula,Embryo,Trunk,Surface Structure
34549,SRR32104354,SRX27449956,SRS23876477,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,24hpf TrunkNC 2,GSM8751789,,source name:trunk NC tissue from somite 7 to somite 16|tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+|geo loc name:missing|collection date:missing,24hpf TrunkNC 2,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,trunk NC tissue from somite 7 to somite 16,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+,GSM8751789,GSM8751789: 24hpf TrunkNC 2; Danio rerio; RNA Seq,GSM8751789 r1,GSM8751789,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10+2_Trunk_24h_19731_R1_combined_filtered.fastq.gz,fastq,1952754850.0,39055097.0,GSM8751789 r1,0:50,A:559564208;C:417671563;G:422591454;T:552829965;N:97660,50,,,,559564208,417671563,422591454,552829965,97660,SRX27449956,SRS23876477,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Pharyngula,Embryo,Trunk,Surface Structure
34550,SRR32104355,SRX27449955,SRS23876476,SRP559533,PRJNA1214751,Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq],GSE287815,Transcriptome Analysis,During vertebrate development  the heart primarily arises from mesoderm  with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives.  Here  by integrating bulk and single cell RNAseq with ATAC seq  we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1  sox9a  tfap2a and ets1. Notably  we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore  expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together  our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination  with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry   were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.,,,,24hpf TrunkNC 1,GSM8751788,,source name:trunk NC tissue from somite 7 to somite 16|tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+|geo loc name:missing|collection date:missing,24hpf TrunkNC 1,Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples,trunk NC tissue from somite 7 to somite 16,,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,tissue:trunk NC tissue from somite 7 to somite 16|cell type:migratory trunk neural crest|transgenic line:Tg 4.9sox10:eGFP|age:24hpf|fluorophore:GFP+,GSM8751788,GSM8751788: 24hpf TrunkNC 1; Danio rerio; RNA Seq,GSM8751788 r1,GSM8751788,1,mch+ CdNC cells and mch  non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected  dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected  dissociated  and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology  Pasadena  CA for 50 million  single ended reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP559533,,,Sox10+1_Trunk_24h_19729_R1_combined_filtered.fastq.gz,fastq,2086584450.0,41731689.0,GSM8751788 r1,0:50,A:588802695;C:455146722;G:460260703;T:582270728;N:103602,50,,,,588802695,455146722,460260703,582270728,103602,SRX27449955,SRS23876476,SRA2058978,"Martik Lab, Molecular and Cell Biology, University of California Berkeley","Martik Lab, Molecular and Cell Biology, University of California Berkeley",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2025-01-23,Pharyngula,Embryo,Trunk,Surface Structure
49611,SRR7989641,SRX4820831,SRS3895222,SRP164769,PRJNA495391,Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling,GSE121041,Transcriptome Analysis,Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO,,pubmed:30451830;pubmed:38570687,,IWR 1 rep3,GSM3424991,,source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,IWR 1 rep3,Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene,brain endothelial cells,,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank’s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,GSM3424991,GSM3424991: IWR 1 rep3; Danio rerio; RNA Seq,GSM3424991,,1,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM3424991,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP164769,,,vanHollebeke_IWR_4_R1.fastq.gz,fastq,2256000713.0,30503539.0,GSM3424991 r1,0:73.96 1:0,A:657293471;C:471495202;G:469388740;T:657813037;N:10263,73,0,,,657293471,471495202,469388740,657813037,10263,SRX4820831,SRS3895222,SRA791232,GEO,MPI for heart and lung research,1,0.82891,,0.22262,,0.78894,,0.52843,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2018-10-09,Pharyngula,Embryo,Multi-tissue,Multi-system
49612,SRR7989640,SRX4820830,SRS3895220,SRP164769,PRJNA495391,Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling,GSE121041,Transcriptome Analysis,Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO,,pubmed:30451830;pubmed:38570687,,IWR 1 rep2,GSM3424990,,source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,IWR 1 rep2,Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene,brain endothelial cells,,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank’s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,GSM3424990,GSM3424990: IWR 1 rep2; Danio rerio; RNA Seq,GSM3424990,,1,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM3424990,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP164769,,,vanHollebeke_IWR_3_R1.fastq.gz,fastq,2320219813.0,31532406.0,GSM3424990 r1,0:73.58 1:0,A:660022378;C:501448817;G:498586533;T:660148405;N:13680,73,0,,,660022378,501448817,498586533,660148405,13680,SRX4820830,SRS3895220,SRA791232,GEO,MPI for heart and lung research,1,0.76766,,0.17893,,0.78206,,0.5236,,74,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2018-10-09,Pharyngula,Embryo,Multi-tissue,Multi-system
49613,SRR7989639,SRX4820829,SRS3895221,SRP164769,PRJNA495391,Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling,GSE121041,Transcriptome Analysis,Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO,,pubmed:30451830;pubmed:38570687,,IWR 1 rep1,GSM3424989,,source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,IWR 1 rep1,Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene,brain endothelial cells,,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank’s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,GSM3424989,GSM3424989: IWR 1 rep1; Danio rerio; RNA Seq,GSM3424989,,1,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM3424989,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP164769,,,vanHollebeke_IWR_1_R1.fastq.gz,fastq,3130301804.0,42242865.0,GSM3424989 r1,0:74.10 1:0,A:906281071;C:658248293;G:654046147;T:911712569;N:13724,74,0,,,906281071,658248293,654046147,911712569,13724,SRX4820829,SRS3895221,SRA791232,GEO,MPI for heart and lung research,1,0.83335,,0.2301,,0.77703,,0.51424,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2018-10-09,Pharyngula,Embryo,Multi-tissue,Multi-system
49614,SRR7989638,SRX4820828,SRS3895223,SRP164769,PRJNA495391,Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling,GSE121041,Transcriptome Analysis,Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO,,pubmed:30451830;pubmed:38570687,,DMSO rep3,GSM3424988,,source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,DMSO rep3,Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene,brain endothelial cells,,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank’s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,GSM3424988,GSM3424988: DMSO rep3; Danio rerio; RNA Seq,GSM3424988,,1,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM3424988,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP164769,,,vanHollebeke_WT_3_R1.fastq.gz,fastq,2942028868.0,39840018.0,GSM3424988 r1,0:73.85 1:0,A:849808636;C:623040120;G:619275913;T:849871928;N:32271,73,0,,,849808636,623040120,619275913,849871928,32271,SRX4820828,SRS3895223,SRA791232,GEO,MPI for heart and lung research,1,0.83348,,0.20415,,0.79147,,0.51054,,74,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2018-10-09,Pharyngula,Embryo,Multi-tissue,Multi-system
49615,SRR7989637,SRX4820827,SRS3895219,SRP164769,PRJNA495391,Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling,GSE121041,Transcriptome Analysis,Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO,,pubmed:30451830;pubmed:38570687,,DMSO rep2,GSM3424987,,source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,DMSO rep2,Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene,brain endothelial cells,,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank’s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,GSM3424987,GSM3424987: DMSO rep2; Danio rerio; RNA Seq,GSM3424987,,1,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM3424987,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP164769,,,vanHollebeke_WT_2_R1.fastq.gz,fastq,2807935583.0,38002656.0,GSM3424987 r1,0:73.89 1:0,A:815631502;C:589381721;G:586257915;T:816652021;N:12424,73,0,,,815631502,589381721,586257915,816652021,12424,SRX4820827,SRS3895219,SRA791232,GEO,MPI for heart and lung research,1,0.84347,,0.20267,,0.77419,,0.51656,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2018-10-09,Pharyngula,Embryo,Multi-tissue,Multi-system
49616,SRR7989636,SRX4820826,SRS3895218,SRP164769,PRJNA495391,Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling,GSE121041,Transcriptome Analysis,Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development  but also relevant for vascular and neurodegenerative diseases. However  beyond the early requirement of Wnt signaling for brain capillary development  there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation.  By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling  we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation.   In the absence of Wnt signaling  premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis  whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO,,pubmed:30451830;pubmed:38570687,,DMSO rep1,GSM3424986,,source name:brain endothelial cells|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,DMSO rep1,Raw reads were assessed for quality  adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “  outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene,brain endothelial cells,,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank’s Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,,lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos|tissue:hindbrain endothelium|age:36hpf,GSM3424986,GSM3424986: DMSO rep1; Danio rerio; RNA Seq,GSM3424986,,1,Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser  5 iterations  50s. post several washes in HBSS Hank's Balanced Salt Solution  Gibco without xxx+/Mg2+  zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged  frozen by liquid nitrogen and stored at  80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.,GEO Accession:GSM3424986,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP164769,,,vanHollebeke_WT_1_R1.fastq.gz,fastq,2675908817.0,36130876.0,GSM3424986 r1,0:74.06 1:0,A:789957205;C:549799082;G:546545868;T:789594811;N:11851,74,0,,,789957205,549799082,546545868,789594811,11851,SRX4820826,SRS3895218,SRA791232,GEO,MPI for heart and lung research,1,0.90594,,0.2159,,0.76765,,0.50407,,75,,B,,usable mapping rate,illumina,nextseq,full_length,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Germany,2018-10-09,Pharyngula,Embryo,Multi-tissue,Multi-system
53504,SRR9879915,SRX6632436,SRS5202043,SRP217196,PRJNA558085,Zebrafish Danio rerio neural crest cell RNA sequencing,GSE135237,Transcriptome Analysis,RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.,,pubmed:31495570,,36hpfNCC rep3,GSM3996851,,source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf,36hpfNCC rep3,For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations,Neural crest cells from larval trunk,36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.,Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing,Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages,tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf,GSM3996851,GSM3996851: 36hpfNCC rep3; Danio rerio; RNA Seq,GSM3996851,,1,Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing,GEO Accession:GSM3996851,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP217196,,,Sample3_S3_R1_001.fastq.gz Sample3_S3_R2_001.fastq.gz,fastq fastq,5670363307.0,19001526.0,GSM3996851 r1,0:149.23 1:149.19,A:1557295113;C:1251445377;G:1252062318;T:1609175566;N:384933,149,149,,,1557295113,1251445377,1252062318,1609175566,384933,SRX6632436,SRS5202043,SRA930488,GEO,"Kucenas Lab, Biology, University of Virginia",2,0.85581,0.858,0.14092,0.14122,0.78784,0.7935,0.55466,0.55065,150,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2019-08-01,Pharyngula,Embryo,Multi-tissue,Multi-system
53505,SRR9879914,SRX6632435,SRS5202042,SRP217196,PRJNA558085,Zebrafish Danio rerio neural crest cell RNA sequencing,GSE135237,Transcriptome Analysis,RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.,,pubmed:31495570,,36hpfNCC rep2,GSM3996850,,source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf,36hpfNCC rep2,For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations,Neural crest cells from larval trunk,36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.,Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing,Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages,tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf,GSM3996850,GSM3996850: 36hpfNCC rep2; Danio rerio; RNA Seq,GSM3996850,,1,Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing,GEO Accession:GSM3996850,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP217196,,,Sample2_S2_R2_001.fastq.gz Sample2_S2_R1_001.fastq.gz,fastq fastq,7936706863.0,26647099.0,GSM3996850 r1,0:148.93 1:148.91,A:2180170247;C:1758018091;G:1758076526;T:2239839139;N:602860,148,148,,,2180170247,1758018091,1758076526,2239839139,602860,SRX6632435,SRS5202042,SRA930488,GEO,"Kucenas Lab, Biology, University of Virginia",2,0.85787,0.85726,0.14387,0.14335,0.7864,0.79123,0.55424,0.54305,150,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2019-08-01,Pharyngula,Embryo,Multi-tissue,Multi-system
53506,SRR9879913,SRX6632434,SRS5202041,SRP217196,PRJNA558085,Zebrafish Danio rerio neural crest cell RNA sequencing,GSE135237,Transcriptome Analysis,RNA sequencing of neural crest cells collected from Gtfoxd3:mCherry;Tgsox10:mEGFP embryos Overall design: foxd3+/sox10+ double positive neural crest cells NCC were collected from the trunk of Gtfoxd3:mCherry;Tgsox10:mEGFP embryos at 36 hpf and 72 hpf and sent for sequencing. 3 replicates for each condition.,,pubmed:31495570,,36hpfNCC rep1,GSM3996849,,source name:Neural crest cells from larval trunk|tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf,36hpfNCC rep1,For data quality control  FASTQC was used to check the raw fastq data quality and Trimmomatic was used to remove adaptors and to trim quality bases. post adapter clipping  we removed leading and trailing ambiguous or low quality bases below Phred quality scores of 3. Trimmomatic works with a user defined window spanning the read from 5′ to 3′ and removes bases only at the 3′ end; we set up a window length of 4 and a quality threshold Q of 20. When the average quality drops below 20  the 3′ end is clipped. The reads were then mapped to the latest UCSC danRer10 transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. Genome build: danRer10 Supplementary files format and content: normalized FPKM counts with annotations,Neural crest cells from larval trunk,36 hpf and 72 hpf Gtfoxd3:mCherry;Tgsox10:mEGFP embryos were chilled in egg water on ice and the anterior halves of the embryos were removed using a scalpel. Trunk pieces were placed in calcium free Ringer’s solution with 2.5mM EDTA and rocked for 15 minutes at 4 °C. The trunk pieces were washed three times with chilled Dulbecco’s PBS D PBS and then transferred to microcentrifuge tubes along with 100ul D PBS. A pellet pestle was used to break up the trunk pieces and then 30ul Liberase TM was added. The samples were incubated for 15 minutes at 28.5 °C  1ml 1x Trypsin with 5% EDTA solution was added  and the samples were incubated for 15 more minutes at 28.5 °C. The samples were pipetted into 5ml D PBS with 1% BSA and then passed through a 40 μm cell strainer and a syringe plunger was used to gently mash the samples into a petri dish. The contents of the petri dish were passed through a new cell strainer and the samples were then transferred to a microcentrifuge tube and were washed 2x with D PBS+BSA. Three samples of cells 1750 ± 750 at each stage were used for RNA sequencing.,Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing,Gtfoxd3:mCherry;Tgsox10:mEGFP zebrafish embryos were raised in egg water at 28.5C to desired stages,tissue:Neural crest cells from larval trunk|transgene:Gtfoxd3:mCherry|transgene:Tgsox10:mEGFP|Stage:36 hpf,GSM3996849,GSM3996849: 36hpfNCC rep1; Danio rerio; RNA Seq,GSM3996849,,1,Qiagen rneasy micro Smartseq v4 Ultra Low Input RNA Kit for Sequencing,GEO Accession:GSM3996849,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP217196,,,Sample1_S1_R1_001.fastq.gz Sample1_S1_R2_001.fastq.gz,fastq fastq,5567367667.0,18627261.0,GSM3996849 r1,0:149.46 1:149.42,A:1451891750;C:1299527629;G:1299734297;T:1515800229;N:413762,149,149,,,1451891750,1299527629,1299734297,1515800229,413762,SRX6632434,SRS5202041,SRA930488,GEO,"Kucenas Lab, Biology, University of Virginia",2,0.70717,0.70612,0.10919,0.10754,0.83366,0.83875,0.55253,0.55519,149,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2019-08-01,Pharyngula,Embryo,Multi-tissue,Multi-system
53598,SRR9961216,SRX6708749,SRS5262464,SRP218232,PRJNA560046,Anterior Posterior gene expression differences in zebrafish Vagus motor neurons,GSE135780,Transcriptome Analysis,We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede expressing Vagus motor neurons  dissecting the posterior hindbrain  dissociating to single cell suspension  and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.,,pubmed:32302545,,PR,GSM4029959,,tissue:Posterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,PR,"Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene level employing the ""intersection strict"" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.",Posterior Vagus motor neurons,,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,GSM4029959,GSM4029959: PR; Danio rerio; RNA Seq,GSM4029959,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029959,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218232,,,PR.R1.fastq.gz PR.R2.fastq.gz,fastq fastq,2401786200.0,24017862.0,GSM4029959 r1,0:50 1:50,A:659290962;C:538233618;G:544650227;T:659578923;N:32470,50,50,,,659290962,538233618,544650227,659578923,32470,SRX6708749,SRS5262464,SRA938975,GEO,Fred Hutchinson Cancer Research Center,2,0.89159,0.90132,0.08505,0.08525,0.79916,0.79997,0.4553,0.4539,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53599,SRR9961215,SRX6708748,SRS5262463,SRP218232,PRJNA560046,Anterior Posterior gene expression differences in zebrafish Vagus motor neurons,GSE135780,Transcriptome Analysis,We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede expressing Vagus motor neurons  dissecting the posterior hindbrain  dissociating to single cell suspension  and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.,,pubmed:32302545,,PG,GSM4029958,,tissue:Posterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,PG,"Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene level employing the ""intersection strict"" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.",Posterior Vagus motor neurons,,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,GSM4029958,GSM4029958: PG; Danio rerio; RNA Seq,GSM4029958,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029958,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218232,,,PG.R1.fastq.gz PG.R2.fastq.gz,fastq fastq,2088408300.0,20884083.0,GSM4029958 r1,0:50 1:50,A:575165459;C:466900649;G:473144365;T:573170304;N:27523,50,50,,,575165459,466900649,473144365,573170304,27523,SRX6708748,SRS5262463,SRA938975,GEO,Fred Hutchinson Cancer Research Center,2,0.87591,0.88321,0.08999,0.0895,0.8099,0.80973,0.4632,0.46188,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53600,SRR9961214,SRX6708747,SRS5262462,SRP218232,PRJNA560046,Anterior Posterior gene expression differences in zebrafish Vagus motor neurons,GSE135780,Transcriptome Analysis,We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede expressing Vagus motor neurons  dissecting the posterior hindbrain  dissociating to single cell suspension  and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.,,pubmed:32302545,,PB,GSM4029957,,tissue:Posterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,PB,"Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene level employing the ""intersection strict"" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.",Posterior Vagus motor neurons,,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,GSM4029957,GSM4029957: PB; Danio rerio; RNA Seq,GSM4029957,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029957,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218232,,,PB.R1.fastq.gz PB.R2.fastq.gz,fastq fastq,1947375800.0,19473758.0,GSM4029957 r1,0:50 1:50,A:540064062;C:431763279;G:436932637;T:538589534;N:26288,50,50,,,540064062,431763279,436932637,538589534,26288,SRX6708747,SRS5262462,SRA938975,GEO,Fred Hutchinson Cancer Research Center,2,0.87385,0.88639,0.10632,0.10717,0.84025,0.84011,0.46398,0.46592,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53601,SRR9961213,SRX6708746,SRS5262461,SRP218232,PRJNA560046,Anterior Posterior gene expression differences in zebrafish Vagus motor neurons,GSE135780,Transcriptome Analysis,We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede expressing Vagus motor neurons  dissecting the posterior hindbrain  dissociating to single cell suspension  and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.,,pubmed:32302545,,AR,GSM4029956,,tissue:Anterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,AR,"Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene level employing the ""intersection strict"" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.",Anterior Vagus motor neurons,,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,GSM4029956,GSM4029956: AR; Danio rerio; RNA Seq,GSM4029956,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029956,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218232,,,AR.R1.fastq.gz AR.R2.fastq.gz,fastq fastq,2384691900.0,23846919.0,GSM4029956 r1,0:50 1:50,A:653468293;C:532843393;G:540027782;T:658320541;N:31891,50,50,,,653468293,532843393,540027782,658320541,31891,SRX6708746,SRS5262461,SRA938975,GEO,Fred Hutchinson Cancer Research Center,2,0.87197,0.87963,0.14589,0.14667,0.78348,0.78539,0.45808,0.46291,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53602,SRR9961212,SRX6708745,SRS5262460,SRP218232,PRJNA560046,Anterior Posterior gene expression differences in zebrafish Vagus motor neurons,GSE135780,Transcriptome Analysis,We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede expressing Vagus motor neurons  dissecting the posterior hindbrain  dissociating to single cell suspension  and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.,,pubmed:32302545,,AG,GSM4029955,,tissue:Anterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,AG,"Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene level employing the ""intersection strict"" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.",Anterior Vagus motor neurons,,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,GSM4029955,GSM4029955: AG; Danio rerio; RNA Seq,GSM4029955,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029955,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218232,,,AG.R1.fastq.gz AG.R2.fastq.gz,fastq fastq,2638571200.0,26385712.0,GSM4029955 r1,0:50 1:50,A:718841383;C:596495936;G:604225667;T:718972746;N:35468,50,50,,,718841383,596495936,604225667,718972746,35468,SRX6708745,SRS5262460,SRA938975,GEO,Fred Hutchinson Cancer Research Center,2,0.85778,0.86626,0.09168,0.09248,0.80079,0.80135,0.47265,0.47114,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53603,SRR9961211,SRX6708744,SRS5262459,SRP218232,PRJNA560046,Anterior Posterior gene expression differences in zebrafish Vagus motor neurons,GSE135780,Transcriptome Analysis,We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28 hpf 30 hpf to identify genes that are differentially expressed between these two cell populations. Overall design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede expressing Vagus motor neurons  dissecting the posterior hindbrain  dissociating to single cell suspension  and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.,,pubmed:32302545,,AB,GSM4029954,,tissue:Anterior Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,AB,"Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene level employing the ""intersection strict"" overlap mode in HTSeq v0.6.1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include counts genreated at the gene level by HTSeq count.",Anterior Vagus motor neurons,,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:28 hpf 30 hpf|genotype:Tgisl1:Kaede,GSM4029954,GSM4029954: AB; Danio rerio; RNA Seq,GSM4029954,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip  covered with mineral oil  and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029954,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218232,,,AB.R1.fastq.gz AB.R2.fastq.gz,fastq fastq,2240766800.0,22407668.0,GSM4029954 r1,0:50 1:50,A:613677740;C:504126555;G:512178339;T:610754298;N:29868,50,50,,,613677740,504126555,512178339,610754298,29868,SRX6708744,SRS5262459,SRA938975,GEO,Fred Hutchinson Cancer Research Center,2,0.87484,0.88129,0.09542,0.0961,0.82008,0.82209,0.46606,0.46753,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53604,SRR9961222,SRX6708755,SRS5262470,SRP218233,PRJNA560048,Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons,GSE135781,Transcriptome Analysis,Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.,,pubmed:32302545,,12 RA,GSM4029965,,tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,12 RA,Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts,Vagus motor neurons,Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,GSM4029965,GSM4029965: 12 RA; Danio rerio; RNA Seq,GSM4029965,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029965,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218233,,,12_RA.R1.fastq.gz 12_RA.R2.fastq.gz,fastq fastq,2411994500.0,24119945.0,GSM4029965 r1,0:50 1:50,A:651875311;C:553371750;G:560482904;T:645562467;N:702068,50,50,,,651875311,553371750,560482904,645562467,702068,SRX6708755,SRS5262470,SRA938976,GEO,Fred Hutchinson Cancer Research Center,2,0.91,0.912,0.0868,0.09489,0.73531,0.74257,0.48209,0.48433,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53605,SRR9961221,SRX6708754,SRS5262469,SRP218233,PRJNA560048,Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons,GSE135781,Transcriptome Analysis,Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.,,pubmed:32302545,,9 RA,GSM4029964,,tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,9 RA,Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts,Vagus motor neurons,Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,GSM4029964,GSM4029964: 9 RA; Danio rerio; RNA Seq,GSM4029964,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029964,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218233,,,9_RA.R1.fastq.gz 9_RA.R2.fastq.gz,fastq fastq,2752434100.0,27524341.0,GSM4029964 r1,0:50 1:50,A:742948333;C:630419013;G:638493678;T:739745278;N:827798,50,50,,,742948333,630419013,638493678,739745278,827798,SRX6708754,SRS5262469,SRA938976,GEO,Fred Hutchinson Cancer Research Center,2,0.91252,0.91511,0.0935,0.09935,0.7303,0.73612,0.48109,0.47973,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53606,SRR9961220,SRX6708753,SRS5262468,SRP218233,PRJNA560048,Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons,GSE135781,Transcriptome Analysis,Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.,,pubmed:32302545,,6 RA,GSM4029963,,tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,6 RA,Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts,Vagus motor neurons,Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,GSM4029963,GSM4029963: 6 RA; Danio rerio; RNA Seq,GSM4029963,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029963,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218233,,,6_RA.R1.fastq.gz 6_RA.R2.fastq.gz,fastq fastq,1950219200.0,19502192.0,GSM4029963 r1,0:50 1:50,A:524892877;C:449943700;G:454069669;T:520743134;N:569820,50,50,,,524892877,449943700,454069669,520743134,569820,SRX6708753,SRS5262468,SRA938976,GEO,Fred Hutchinson Cancer Research Center,2,0.91139,0.91465,0.08909,0.0985,0.72665,0.73539,0.48694,0.49354,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53607,SRR9961219,SRX6708752,SRS5262467,SRP218233,PRJNA560048,Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons,GSE135781,Transcriptome Analysis,Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.,,pubmed:32302545,,10 DMSO,GSM4029962,,tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,10 DMSO,Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts,Vagus motor neurons,Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,GSM4029962,GSM4029962: 10 DMSO; Danio rerio; RNA Seq,GSM4029962,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029962,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218233,,,10_DMSO.R1.fastq.gz 10_DMSO.R2.fastq.gz,fastq fastq,2564610000.0,25646100.0,GSM4029962 r1,0:50 1:50,A:695263400;C:585667319;G:591832017;T:691080534;N:766730,50,50,,,695263400,585667319,591832017,691080534,766730,SRX6708752,SRS5262467,SRA938976,GEO,Fred Hutchinson Cancer Research Center,2,0.89865,0.90128,0.09345,0.1017,0.73805,0.74683,0.4764,0.47485,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53608,SRR9961218,SRX6708751,SRS5262466,SRP218233,PRJNA560048,Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons,GSE135781,Transcriptome Analysis,Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.,,pubmed:32302545,,4 DMSO,GSM4029961,,tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,4 DMSO,Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts,Vagus motor neurons,Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,GSM4029961,GSM4029961: 4 DMSO; Danio rerio; RNA Seq,GSM4029961,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029961,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218233,,,4_DMSO.R1.fastq.gz 4_DMSO.R2.fastq.gz,fastq fastq,2944532300.0,29445323.0,GSM4029961 r1,0:50 1:50,A:794249480;C:674151778;G:684114554;T:791128243;N:888245,50,50,,,794249480,674151778,684114554,791128243,888245,SRX6708751,SRS5262466,SRA938976,GEO,Fred Hutchinson Cancer Research Center,2,0.89952,0.9014,0.0972,0.10304,0.73166,0.73862,0.47176,0.47741,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
53609,SRR9961217,SRX6708750,SRS5262465,SRP218233,PRJNA560048,Gene expression changes in Retinoic Acid treated zebrafish Vagus motor neurons,GSE135781,Transcriptome Analysis,Weprofiled the transcriptomes of DMSO treated control and Retinoic Acid treated zebrafish Vagus motor neurons at 38 hpf to identifiy genes that are differentially expressed between these two treatments. Overall design: We obtained cells by dissecting the hindbrains of Tgisl1:Kaede expressing embryos  dissociating to single cell suspension  and sorting for Kaede positive cells by flow cytometry.  We sequenced 3 replicates of 4500 10000 cells per condition.,,pubmed:32302545,,1 DMSO,GSM4029960,,tissue:Vagus motor neurons|cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,1 DMSO,Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software  followed by 'demultiplexing' of indexed reads and generation of FASTQ files  using Illumina's bcl2fastq v1.8.4 Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2 pass mode.  Counts were generated from STAR alignments at the gene level using featureCounts from the Subread package v1.5.0. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include counts generated at the gene level by featureCounts,Vagus motor neurons,Embryos were treated 0.2mM PTU  as well as with 50nM Retinoic Acid in DMSO  or the equivalent volumen of DMSO as a control  beginning at 24hpf.,The posterior hindbrain was manually dissected in calcium free Ringer’s solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,,cell type:Vagus motor neurons|developmental stage:38 hpf|genotype:Tgisl1:Kaede,GSM4029960,GSM4029960: 1 DMSO; Danio rerio; RNA Seq,GSM4029960,,1,The posterior hindbrain was manually dissected in calcium free Ringer's solution with MESAB  and dissected tissue was dissociated to single cell suspension by pipetting in 0.25%Trypsin EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+  DAPI  cells were collected in lysis buffer from the RNA isolation kit and immediately processed. RNA was isolated using the RNAqueous Micro Total RNA Isolation Kit  cDNA was amplified using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing  and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.,GEO Accession:GSM4029960,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP218233,,,1_DMSO.R1.fastq.gz 1_DMSO.R2.fastq.gz,fastq fastq,2672431200.0,26724312.0,GSM4029960 r1,0:50 1:50,A:730227451;C:600836649;G:608011607;T:732560809;N:794684,50,50,,,730227451,600836649,608011607,732560809,794684,SRX6708750,SRS5262465,SRA938976,GEO,Fred Hutchinson Cancer Research Center,2,0.89002,0.89327,0.11786,0.12268,0.73379,0.73874,0.47942,0.48107,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2019-08-13,Pharyngula,Embryo,Brain,Nervous System
55866,SRR10863008,SRX7533061,SRS5972270,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep4,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,wt PGCs 1dpf S1,wt PGCs 1dpf S1,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,NextSeq 550,,SRP241074,,,wt_PGCs_1dpf_S1.R1.fastq.gz,fastq,6787337699.0,81775153.0,wt PGCs 1dpf S1.R1.fastq.gz,0:83 1:0,A:1839754910;C:1566044514;G:1538211923;T:1843241243;N:85109,83,0,,,1839754910,1566044514,1538211923,1843241243,85109,SRX7533061,SRS5972270,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,1,0.94441,,0.056,,0.68866,,0.47945,,83,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55880,SRR10863022,SRX7533047,SRS5972268,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep3,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3,imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_03_20_1dpf_PGCs_rep3_S3.R2.fastq.gz,fastq fastq,3406105382.0,21557629.0,imb ketting 2018 02 redl SmartSeq 03 20 1dpf PGCs rep3 S3.R1.fastq.gz,0:79 1:79,A:914561772;C:790081165;G:768217890;T:933018206;N:226349,79,79,,,914561772,790081165,768217890,933018206,226349,SRX7533047,SRS5972268,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.93859,0.93927,0.06346,0.06362,0.68467,0.68665,0.51016,0.44765,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55881,SRR10863023,SRX7533046,SRS5972267,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2,imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_02_30_1dpf_PGCs_rep2_S2.R2.fastq.gz,fastq fastq,3126220074.0,19786203.0,imb ketting 2018 02 redl SmartSeq 02 30 1dpf PGCs rep2 S2.R1.fastq.gz,0:79 1:79,A:835660285;C:727271703;G:711392935;T:851683391;N:211760,79,79,,,835660285,727271703,711392935,851683391,211760,SRX7533046,SRS5972267,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.93836,0.93845,0.05796,0.0579,0.67805,0.68002,0.49555,0.49733,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55885,SRR10863024,SRX7533042,SRS5972265,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt PGCs 1dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: PGCs 1dpf,imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1,imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_01_24_1dpf_PGCs_rep1_S1.R2.fastq.gz,fastq fastq,3512354852.0,22230094.0,imb ketting 2018 02 redl SmartSeq 01 24 1dpf PGCs rep1 S1.R1.fastq.gz,0:79 1:79,A:937439392;C:820724988;G:797835842;T:956108725;N:245905,79,79,,,937439392,820724988,797835842,956108725,245905,SRX7533042,SRS5972265,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.94053,0.94062,0.05733,0.05792,0.6801,0.68174,0.49423,0.49408,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55895,SRR10863036,SRX7533032,SRS5972257,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt Fish 1dpf rep2,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: Fish 1dpf,imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14,imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_14_69_1dpf_Fish_rep2_S14.R2.fastq.gz,fastq fastq,3173577572.0,20085934.0,imb ketting 2018 02 redl SmartSeq 14 69 1dpf Fish rep2 S14.R1.fastq.gz,0:79 1:79,A:851665093;C:736131084;G:718748661;T:866816699;N:216035,79,79,,,851665093,736131084,718748661,866816699,216035,SRX7533032,SRS5972257,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.94469,0.9439,0.08631,0.08612,0.71062,0.71204,0.46629,0.46237,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
55896,SRR10863037,SRX7533031,SRS5972256,SRP241074,PRJNA597223,Danio rerio primordial germ cell expression pofiling,PRJNA597223,Whole Genome Sequencing,Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.,,,The vasa:eGFP line Krøvel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80°C until library preparation was done.,,wt Fish 1dpf rep1,,strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,mRNA of Zebrafish: Fish 1dpf,imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13,imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13,Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 550,,SRP241074,,,imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_13_01_1dpf_Fish_rep1_S13.R2.fastq.gz,fastq fastq,3241792492.0,20517674.0,imb ketting 2018 02 redl SmartSeq 13 01 1dpf Fish rep1 S13.R1.fastq.gz,0:79 1:79,A:865936682;C:756362974;G:735614291;T:883655547;N:222998,79,79,,,865936682,756362974,735614291,883655547,222998,SRX7533031,SRS5972256,SRA1023320,Rene Ketting group|Ketting Lab,Rene Ketting group,2,0.94544,0.94715,0.08154,0.0819,0.70928,0.71011,0.45932,0.46165,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_plate,smartseq,,Germany,2020-01-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
59051,SRR11585437,SRX8152990,SRS6515540,SRP257811,PRJNA627266,Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks,GSE149081,Transcriptome Analysis,Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.,,pubmed:32867764;pubmed:35286299,,PEC MUT 3,GSM4490217,,source name:Pancreatic endocrine cells PECs|strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Pax6b / ,PEC MUT 3,Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample,Pancreatic endocrine cells PECs,The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.,strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Pax6b / ,GSM4490217,GSM4490217: PEC MUT 3; Danio rerio; RNA Seq,GSM4490217,,1,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,GEO Accession:GSM4490217,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP257811,,,NGS14-B707_T_TAGGCATG_L004_R1_001.fastq.gz NGS14-B707_T_TAGGCATG_L004_R2_001.fastq.gz,fastq fastq,9748511112.0,48259956.0,GSM4490217 r1,0:101 1:101,A:2803666267;C:2055025246;G:1963563755;T:2899642984;N:26612860,101,101,,,2803666267,2055025246,1963563755,2899642984,26612860,SRX8152990,SRS6515540,SRA1067841,GEO,"GIGA, University of Liège",2,0.87356,0.86714,0.23052,0.2277,0.75615,0.75848,0.43909,0.54379,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2020-04-21,Pharyngula,Embryo,Pancreas,Endocrine System
59052,SRR11585436,SRX8152989,SRS6515539,SRP257811,PRJNA627266,Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks,GSE149081,Transcriptome Analysis,Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.,,pubmed:32867764;pubmed:35286299,,PEC MUT 2,GSM4490216,,source name:Pancreatic endocrine cells PECs|strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Pax6b / ,PEC MUT 2,Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample,Pancreatic endocrine cells PECs,The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.,strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Pax6b / ,GSM4490216,GSM4490216: PEC MUT 2; Danio rerio; RNA Seq,GSM4490216,,1,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,GEO Accession:GSM4490216,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP257811,,,NGS14-B706_R_S_GGACTCCT_L004_R1_001.fastq.gz NGS14-B706_R_S_GGACTCCT_L004_R2_001.fastq.gz,fastq fastq,8955505370.0,44334185.0,GSM4490216 r1,0:101 1:101,A:2528403855;C:1932514267;G:1792623469;T:2677457686;N:24506093,101,101,,,2528403855,1932514267,1792623469,2677457686,24506093,SRX8152989,SRS6515539,SRA1067841,GEO,"GIGA, University of Liège",2,0.86059,0.85263,0.22423,0.22202,0.76037,0.76341,0.57108,0.57284,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2020-04-21,Pharyngula,Embryo,Pancreas,Endocrine System
59053,SRR11585435,SRX8152988,SRS6515538,SRP257811,PRJNA627266,Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks,GSE149081,Transcriptome Analysis,Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.,,pubmed:32867764;pubmed:35286299,,PEC MUT 1,GSM4490215,,source name:Pancreatic endocrine cells PECs|strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Pax6b / ,PEC MUT 1,Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample,Pancreatic endocrine cells PECs,The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.,strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Pax6b / ,GSM4490215,GSM4490215: PEC MUT 1; Danio rerio; RNA Seq,GSM4490215,,1,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,GEO Accession:GSM4490215,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP257811,,,NGS14-B705_P_Q_AGGCAGAA_L004_R1_001.fastq.gz NGS14-B705_P_Q_AGGCAGAA_L004_R2_001.fastq.gz,fastq fastq,13479804612.0,66731706.0,GSM4490215 r1,0:101 1:101,A:3797860443;C:2925701277;G:2742725489;T:3976642053;N:36875350,101,101,,,3797860443,2925701277,2742725489,3976642053,36875350,SRX8152988,SRS6515538,SRA1067841,GEO,"GIGA, University of Liège",2,0.86774,0.8597,0.24744,0.2445,0.76144,0.76424,0.47271,0.47375,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2020-04-21,Pharyngula,Embryo,Pancreas,Endocrine System
59054,SRR11585434,SRX8152987,SRS6515537,SRP257811,PRJNA627266,Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks,GSE149081,Transcriptome Analysis,Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.,,pubmed:32867764;pubmed:35286299,,PEC WT 3,GSM4490214,,source name:Pancreatic endocrine cells PECs|strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Wild type,PEC WT 3,Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample,Pancreatic endocrine cells PECs,The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.,strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Wild type,GSM4490214,GSM4490214: PEC WT 3; Danio rerio; RNA Seq,GSM4490214,,1,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,GEO Accession:GSM4490214,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP257811,,,NGS14-B660_smarter2_nextera_CGTACTAG_L006_R2_001.fastq.gz NGS14-B660_smarter2_nextera_CGTACTAG_L006_R1_001.fastq.gz,fastq fastq,20654948000.0,103274740.0,GSM4490214 r1,0:100 1:100,A:5802500159;C:4458409088;G:4231724469;T:6065636461;N:96677823,100,100,,,5802500159,4458409088,4231724469,6065636461,96677823,SRX8152987,SRS6515537,SRA1067841,GEO,"GIGA, University of Liège",2,0.86031,0.86065,0.19435,0.19471,0.75422,0.75513,0.52743,0.52416,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2020-04-21,Pharyngula,Embryo,Pancreas,Endocrine System
59055,SRR11585433,SRX8152986,SRS6515536,SRP257811,PRJNA627266,Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks,GSE149081,Transcriptome Analysis,Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.,,pubmed:32867764;pubmed:35286299,,PEC WT 2,GSM4490213,,source name:Pancreatic endocrine cells PECs|strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Wild type,PEC WT 2,Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample,Pancreatic endocrine cells PECs,The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.,strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Wild type,GSM4490213,GSM4490213: PEC WT 2; Danio rerio; RNA Seq,GSM4490213,,1,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,GEO Accession:GSM4490213,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP257811,,,NGS14-B808_G_TCCTGAGC_L008_R1_001.fastq.gz NGS14-B808_G_TCCTGAGC_L008_R2_001.fastq.gz,fastq fastq,10503079890.0,51995445.0,GSM4490213 r1,0:101 1:101,A:2976843650;C:2276866070;G:2085770808;T:3145487654;N:18111708,101,101,,,2976843650,2276866070,2085770808,3145487654,18111708,SRX8152986,SRS6515536,SRA1067841,GEO,"GIGA, University of Liège",2,0.86353,0.86275,0.20842,0.20846,0.77684,0.778,0.58056,0.58259,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2020-04-21,Pharyngula,Embryo,Pancreas,Endocrine System
59056,SRR11585432,SRX8152985,SRS6515535,SRP257811,PRJNA627266,Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks,GSE149081,Transcriptome Analysis,Background: Endocrine cells of the digestive system  including the pancreatic endocrine cells PECs clustered in the islets of Langerhans and the enteroendocrine cells EECs scattered in the intestinal epithelium  play an important role in metabolism. Although EECs and PECs are located in distinct organs  they share many features and several common genes control their differentiation.  In this study  we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory networks controlled by pax6b  a key player in both EECs and PECs. Results: RNA sequencing was performed on EECs and PECs isolated from wild type and pax6b mutant zebrafish. Data mining of wild type zebrafish EEC data confirmed the expression of orthologs for most known mammalian EEC hormones but also revealed the expression of three additional neuropeptide hormones Proenkephalin a  Calcitonin a and Adcyap1a not yet reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs  PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs  with more than 70 % of genes being expressed in both endocrine cell types. Comparison of Pax6b regulated genes in EECs and PECs revealed a significant overlap.  pax6b loss of function does not affect the total number of EECs and PECs but instead disrupts the balance between cell subtypes  leading to an increase of ghrelin  and motilin like expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta  and delta cells in the pancreas and pyyb expressing cells in the intestine. Finally  we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. Conclusion:  This study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels  supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as Type 2 diabetes. Overall design: RNA sequencing of 13 samples. Pancreatic endocrine cell pax6b:GFP + transcriptomic profiles of 27 hpf wild type WT and pax6b /  MUT zebrafish embryos were generated in triplicates. Enteroendocrine cell pax6b:GFP + transcriptomic profiles of 4d wild type WT and pax6b /  MUT zebrafish emryos were generated in 4 replicates and 3 replicates  respectively.,,pubmed:32867764;pubmed:35286299,,PEC WT 1,GSM4490212,,source name:Pancreatic endocrine cells PECs|strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Wild type,PEC WT 1,Sequences were trimmed in order to remove adaptors and low quality bases Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b Dobin et al.  2013 and gene expression was measured from the mapped reads by using built in STAR module   quantMode GeneCounts. Genome build: GRCz11   release 92 Ensembl Supplementary files format and content: tab delimited text files include raw counts for annotations for each Sample,Pancreatic endocrine cells PECs,The following zebrafish transgenic and mutant lines were used: Tgpax6b:GFPulg515 Delporte et al.  2008b  TgBACpdx1:EGFPbns13 Helker et al.  2019  TG 8.5nkx2.2a:GFPia2 Pauls et al.  2007  pax6bsa0086 and pax6bsunrise Verbruggen et al.  2010.,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,Zebrafish Danio rerio were raised according to standard protocols and staged according to Kimmel Kimmel et al.  1995.,strain:AB|tissue:Endocrine pancreas|age:27 hpf|genotype:Wild type,GSM4490212,GSM4490212: PEC WT 1; Danio rerio; RNA Seq,GSM4490212,,1,Enteroendocrine cells EECs were isolated by dissecting the gut from about 200 Tgpax6b:GFPulg515 larvae at 4 dpf  taking care of not including pancreatic tissue. Cell dissociation was next performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase Life Technologies for 10 minutes. Cells were washed in HBSS Mg2+ and Ca2+ free containing  1% BSA and GFP expressing EECs were selected by two consecutive FACS purifications  the first in the “yield mode” and the second in “the purity mode”  using FACS Aria II. Four replicates of EEC containing about 3000 cells were prepared. Pancreatic endocrine cells PECs were also obtained from the Tgpax6b:GFPulg515 line Delporte et al.  2008b by dissecting the dorsal pancreatic bud from about 200 hpf 27 hpf transgenic embryos. FACS selection was performed as described for EECs except that cell dissociation was performed in Tryple Select 1X  Gibco supplemented with 100 U/ml collagenase IV Life Technologies for 5 minutes. For the preparations of EECs and PECs from pax6b null mutant embryos  the pax6sa0086 line  Verbruggen et al.  2010 was first crossed with the Tgpax6b:GFPulg515 line; heterozygous pax6bsa0086 fish harboring the transgene pax6b:GFP were inbred to generate homozygous pax6bsa0086  transgenic embryos which were selected based on the absence or reduction of lens. The isolation of EECs and PECs from pax6bsa0086 homozygous were performed in triplicates following the same procedure than for the wild type larvae. The accuracy of pax6bsa0086 homozygous selection was verified post the RNA seq by checking the presence of the null sa0086 allele in 100% of pax6b reads in the mutant samples. Each EEC or PEC sample obtained post FACS was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer  lysed by freezing in liquid nitrogen and stored at  80°C according the the Smart seq2 protocol Picelli et al.  2014. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay Agilent technologies. 1 ng cDNA was used for preparing each cDNA library using Nextera XT kit Illumina and sequenced on Hi seq 2000 to obtain around 60 millions of reads 100 base paired ends.,GEO Accession:GSM4490212,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP257811,,,NGS14-B807_W_GGACTCCT_L007_R1_001.fastq.gz NGS14-B807_W_GGACTCCT_L007_R2_001.fastq.gz,fastq fastq,14677951452.0,72663126.0,GSM4490212 r1,0:101 1:101,A:4224653583;C:3102454516;G:2862142913;T:4464917832;N:23782608,101,101,,,4224653583,3102454516,2862142913,4464917832,23782608,SRX8152985,SRS6515535,SRA1067841,GEO,"GIGA, University of Liège",2,0.86214,0.86117,0.23896,0.23862,0.77518,0.7777,0.56108,0.57109,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2020-04-21,Pharyngula,Embryo,Pancreas,Endocrine System
59119,SRR11684011,SRX8244814,SRS6592451,SRP259988,PRJNA630160,Zebrafish embryonic mpeg+ macrophages,GSE149786,Transcriptome Analysis,We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates,parent bioproject:PRJNA630158,pubmed:32367800,,csf1r doubleknockout3 28hpf,GSM4512703,,tissue:whole embryos|developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells,csf1r doubleknockout3 28hpf,Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks  v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.,whole embryos,,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle,developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells,GSM4512703,GSM4512703: csf1r doubleknockout3 28hpf; Danio rerio; RNA Seq,GSM4512703,,1,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4512703,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP259988,,intentional duplicate,csf1r_doubleknockout3_28hpf.bam,bam,2776983342.0,18329912.0,GSM4512703 r1,0:75.96 1:75.54,A:776587586;C:613125618;G:616153519;T:757439274;N:13677345,75,75,,,776587586,613125618,616153519,757439274,13677345,SRX8244814,SRS6592451,SRA1072139,GEO,Erasmus MC,2,0.92512,0.93371,0.1054,0.10799,0.78307,0.78287,0.44838,0.44486,76,76,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,trueseq,sc,single_cell_plate,smartseq,,Netherlands,2020-05-04,Pharyngula,Embryo,Whole Organism,All anatomical structures
59120,SRR11684010,SRX8244813,SRS6592450,SRP259988,PRJNA630160,Zebrafish embryonic mpeg+ macrophages,GSE149786,Transcriptome Analysis,We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates,parent bioproject:PRJNA630158,pubmed:32367800,,csf1r doubleknockout2 28hpf,GSM4512702,,tissue:whole embryos|developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells,csf1r doubleknockout2 28hpf,Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks  v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.,whole embryos,,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle,developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells,GSM4512702,GSM4512702: csf1r doubleknockout2 28hpf; Danio rerio; RNA Seq,GSM4512702,,1,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4512702,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP259988,,intentional duplicate,csf1r_doubleknockout2_28hpf.bam,bam,2908203540.0,19226046.0,GSM4512702 r1,0:75.97 1:75.30,A:812002267;C:642558682;G:646762399;T:792733574;N:14146618,75,75,,,812002267,642558682,646762399,792733574,14146618,SRX8244813,SRS6592450,SRA1072139,GEO,Erasmus MC,2,0.92454,0.93402,0.10684,0.11073,0.78238,0.78224,0.44909,0.44853,76,76,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,trueseq,sc,single_cell_plate,smartseq,,Netherlands,2020-05-04,Pharyngula,Embryo,Whole Organism,All anatomical structures
59121,SRR11684009,SRX8244812,SRS6592449,SRP259988,PRJNA630160,Zebrafish embryonic mpeg+ macrophages,GSE149786,Transcriptome Analysis,We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates,parent bioproject:PRJNA630158,pubmed:32367800,,csf1r doubleknockout1 28hpf,GSM4512701,,tissue:whole embryos|developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells,csf1r doubleknockout1 28hpf,Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks  v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.,whole embryos,,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle,developmental stage:28 hpf|genotype/variation:csf1raj4e1/j4e1;csf1rbre01/re01 tgmpeg GFP|cell type:mpeg GFP+ cells,GSM4512701,GSM4512701: csf1r doubleknockout1 28hpf; Danio rerio; RNA Seq,GSM4512701,,1,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4512701,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP259988,,intentional duplicate,csf1r_doubleknockout1_28hpf.bam,bam,1613198946.0,10660488.0,GSM4512701 r1,0:75.96 1:75.37,A:450889241;C:356351947;G:358636604;T:439481905;N:7839249,75,75,,,450889241,356351947,358636604,439481905,7839249,SRX8244812,SRS6592449,SRA1072139,GEO,Erasmus MC,2,0.92472,0.93343,0.10689,0.10892,0.77784,0.77686,0.45013,0.45869,76,76,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,trueseq,sc,single_cell_plate,smartseq,,Netherlands,2020-05-04,Pharyngula,Embryo,Whole Organism,All anatomical structures
59122,SRR11684008,SRX8244811,SRS6592448,SRP259988,PRJNA630160,Zebrafish embryonic mpeg+ macrophages,GSE149786,Transcriptome Analysis,We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates,parent bioproject:PRJNA630158,pubmed:32367800,,wildtype cntr3 28hpf,GSM4512700,,tissue:whole embryos|developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells,wildtype cntr3 28hpf,Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks  v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.,whole embryos,,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle,developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells,GSM4512700,GSM4512700: wildtype cntr3 28hpf; Danio rerio; RNA Seq,GSM4512700,,1,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4512700,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP259988,,intentional duplicate,wildtype_cntr3_28hpf.bam,bam,2994589195.0,19843035.0,GSM4512700 r1,0:75.96 1:74.95,A:831532991;C:665759016;G:671898629;T:810655335;N:14743224,75,74,,,831532991,665759016,671898629,810655335,14743224,SRX8244811,SRS6592448,SRA1072139,GEO,Erasmus MC,2,0.93121,0.93827,0.09775,0.09985,0.77861,0.77889,0.45486,0.4521,76,76,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,trueseq,sc,single_cell_plate,smartseq,,Netherlands,2020-05-04,Pharyngula,Embryo,Whole Organism,All anatomical structures
59123,SRR11684007,SRX8244810,SRS6592447,SRP259988,PRJNA630160,Zebrafish embryonic mpeg+ macrophages,GSE149786,Transcriptome Analysis,We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates,parent bioproject:PRJNA630158,pubmed:32367800,,wildtype cntr2 28hpf,GSM4512699,,tissue:whole embryos|developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells,wildtype cntr2 28hpf,Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks  v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.,whole embryos,,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle,developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells,GSM4512699,GSM4512699: wildtype cntr2 28hpf; Danio rerio; RNA Seq,GSM4512699,,1,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4512699,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP259988,,intentional duplicate,wildtype_cntr2_28hpf.bam,bam,2714096863.0,17970580.0,GSM4512699 r1,0:75.96 1:75.07,A:753731545;C:603594075;G:608442658;T:735104220;N:13224365,75,75,,,753731545,603594075,608442658,735104220,13224365,SRX8244810,SRS6592447,SRA1072139,GEO,Erasmus MC,2,0.93052,0.93777,0.09537,0.09754,0.7806,0.78094,0.45674,0.46243,76,76,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,trueseq,sc,single_cell_plate,smartseq,,Netherlands,2020-05-04,Pharyngula,Embryo,Whole Organism,All anatomical structures
59124,SRR11684006,SRX8244809,SRS6592446,SRP259988,PRJNA630160,Zebrafish embryonic mpeg+ macrophages,GSE149786,Transcriptome Analysis,We used zebrafish lacking functional csf1r to unravel how and when csf1r is necessary for the development of early tissue macrophages from embryonic macrophages. Transcriptomic analysis of mpeg+ macrophages revealed that csf1r deficient macrophages show a macrophage transcriptome  but reduced expression of cell cycle and RNA/DNA metabolism related genes. Transcriptional changes over time were similar between wildtype controls als csf1r deficient embryonic macrophages. Overall design: Bulk RNA sequencing of embyonic macrophages obtained from wildtype control and csf1rDM zebrafish embryos at 28 hpf and 50 hpf in triplicates,parent bioproject:PRJNA630158,pubmed:32367800,,wildtype cntr1 28hpf,GSM4512698,,tissue:whole embryos|developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells,wildtype cntr1 28hpf,Sequencing and base calling was performed on the Illumina hiseq 2500. Resulting base calls were de multiplexed using the Illumina Casava 1.8 software. Subsequently SMARTer adapters were removed using cutadapt followed by the alignment step using STAR version 2.5.4b. Reference genome build GRCz10 danRer10 was used. Abundance estimation was performed using cufflinks  v2.2.1 with both the frag bias correct and multi read correct flags set. The raw read counts were measured using HTSeq count version 0.11.0. using the union setting. The ensemble gene database was used. The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges Lawrence et al. Plos Computational Biology  2013. Differential gene expression analysis was performed with Bioconductor package EdgeR Robinson  et al.  2010. Genome build: GRCz10 Supplementary files format and content: CPM values [.csv] semicolon delimited files.,whole embryos,,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,HEPES buffered E3 medium 28 degrees celsius 14/10h light/dark cycle,developmental stage:28 hpf|genotype/variation:wildtype tgmpeg GFP|cell type:mpeg GFP+ cells,GSM4512698,GSM4512698: wildtype cntr1 28hpf; Danio rerio; RNA Seq,GSM4512698,,1,35 embryos 28 hpf wt  50 hpf wt  28 hpf csf1rdm or 70 embryos csf1rdm 50 hpf were pooled per replicate sample and dissociated with trypsin on ice. mpeg GFP+ cells were FAC sorted directly into Trizol reagent. RNA was harvested using Trizol reagent. cDNA amplification: SMART seq V4 ultra low input RNA kit for sequencing Takara BIO USA  Inc.. Illumina Truseq Sample Preparation V.2 guide was used and the samples were paired end sequenced 2x75 bp on the Illumina HiSeq 2500. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4512698,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP259988,,intentional duplicate,wildtype_cntr1_28hpf.bam,bam,2326310736.0,15392307.0,GSM4512698 r1,0:75.96 1:75.18,A:647113553;C:516650373;G:520662730;T:630666248;N:11217832,75,75,,,647113553,516650373,520662730,630666248,11217832,SRX8244809,SRS6592446,SRA1072139,GEO,Erasmus MC,2,0.93181,0.93856,0.09723,0.10044,0.77333,0.77285,0.45198,0.45136,76,76,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,trueseq,sc,single_cell_plate,smartseq,,Netherlands,2020-05-04,Pharyngula,Embryo,Whole Organism,All anatomical structures
63453,SRR13839922,SRX10218312,SRS8362898,SRP309041,PRJNA706190,Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling,GSE168131,Transcriptome Analysis,The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS.,parent bioproject:PRJNA706402,pubmed:34936864,,Low Wnt NC cells 3,GSM5129522,,tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt,Low Wnt NC cells 3,reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample,FACS sorted NC cells,,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,,genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt,GSM5129522,GSM5129522: Low Wnt NC cells 3; Danio rerio; RNA Seq,GSM5129522,,1,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,GEO Accession:GSM5129522,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP309041,,loader:fastq load.py,nR032-L4-G1-P015-TAGGCA-READ1-Sequences.txt nR032-L4-G1-P015-TAGGCA-READ2-Sequences.txt,fastq fastq,3147743578.0,15582889.0,GSM5129522 r1,0:101 1:101,A:781284855;C:806136762;G:712532566;T:847730332;N:59063,101,101,,,781284855,806136762,712532566,847730332,59063,SRX10218312,SRS8362898,SRA1202348,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",2,0.93267,0.93417,0.0531,0.05308,0.75243,0.75097,0.45171,0.44907,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
63454,SRR13839921,SRX10218311,SRS8362897,SRP309041,PRJNA706190,Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling,GSE168131,Transcriptome Analysis,The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS.,parent bioproject:PRJNA706402,pubmed:34936864,,Low Wnt NC cells 2,GSM5129521,,tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt,Low Wnt NC cells 2,reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample,FACS sorted NC cells,,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,,genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt,GSM5129521,GSM5129521: Low Wnt NC cells 2; Danio rerio; RNA Seq,GSM5129521,,1,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,GEO Accession:GSM5129521,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP309041,,loader:fastq load.py,nR032-L4-G1-P014-GGACTC-READ1-Sequences.txt nR032-L4-G1-P014-GGACTC-READ2-Sequences.txt,fastq fastq,4362163538.0,21594869.0,GSM5129521 r1,0:101 1:101,A:1089673450;C:1110192310;G:1011583336;T:1150590545;N:123897,101,101,,,1089673450,1110192310,1011583336,1150590545,123897,SRX10218311,SRS8362897,SRA1202348,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",2,0.85774,0.85776,0.04869,0.04855,0.76648,0.76676,0.53104,0.5294,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
63455,SRR13839920,SRX10218310,SRS8362895,SRP309041,PRJNA706190,Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling,GSE168131,Transcriptome Analysis,The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS.,parent bioproject:PRJNA706402,pubmed:34936864,,Low Wnt NC cells 1,GSM5129520,,tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt,Low Wnt NC cells 1,reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample,FACS sorted NC cells,,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,,genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:Low Wnt,GSM5129520,GSM5129520: Low Wnt NC cells 1; Danio rerio; RNA Seq,GSM5129520,,1,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,GEO Accession:GSM5129520,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP309041,,loader:fastq load.py,nR032-L4-G1-P013-TCCTGA-READ1-Sequences.txt nR032-L4-G1-P013-TCCTGA-READ2-Sequences.txt,fastq fastq,3857437450.0,19096225.0,GSM5129520 r1,0:101 1:101,A:929676756;C:1024088841;G:880029487;T:1023570451;N:71915,101,101,,,929676756,1024088841,880029487,1023570451,71915,SRX10218310,SRS8362895,SRA1202348,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",2,0.93694,0.94084,0.0529,0.05308,0.76161,0.76079,0.51761,0.52186,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
63456,SRR13839919,SRX10218309,SRS8362896,SRP309041,PRJNA706190,Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling,GSE168131,Transcriptome Analysis,The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS.,parent bioproject:PRJNA706402,pubmed:34936864,,High Wnt NC cells 3,GSM5129519,,tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt,High Wnt NC cells 3,reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample,FACS sorted NC cells,,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,,genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt,GSM5129519,GSM5129519: High Wnt NC cells 3; Danio rerio; RNA Seq,GSM5129519,,1,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,GEO Accession:GSM5129519,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP309041,,loader:fastq load.py,nR032-L4-G1-P012-AGGCAG-READ1-Sequences.txt nR032-L4-G1-P012-AGGCAG-READ2-Sequences.txt,fastq fastq,3730572764.0,18468182.0,GSM5129519 r1,0:101 1:101,A:921867106;C:966471686;G:873294872;T:968868980;N:70120,101,101,,,921867106,966471686,873294872,968868980,70120,SRX10218309,SRS8362896,SRA1202348,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",2,0.94691,0.94912,0.05558,0.0555,0.75475,0.7539,0.53159,0.53741,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
63457,SRR13839918,SRX10218308,SRS8362894,SRP309041,PRJNA706190,Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling,GSE168131,Transcriptome Analysis,The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS.,parent bioproject:PRJNA706402,pubmed:34936864,,High Wnt NC cells 2,GSM5129518,,tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt,High Wnt NC cells 2,reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample,FACS sorted NC cells,,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,,genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt,GSM5129518,GSM5129518: High Wnt NC cells 2; Danio rerio; RNA Seq,GSM5129518,,1,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,GEO Accession:GSM5129518,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP309041,,loader:fastq load.py,nR032-L4-G1-P011-CGTACT-READ1-Sequences.txt nR032-L4-G1-P011-CGTACT-READ2-Sequences.txt,fastq fastq,3605408110.0,17848555.0,GSM5129518 r1,0:101 1:101,A:885541901;C:935723298;G:827921325;T:956154180;N:67406,101,101,,,885541901,935723298,827921325,956154180,67406,SRX10218308,SRS8362894,SRA1202348,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",2,0.94463,0.94671,0.0489,0.04859,0.75694,0.75564,0.51745,0.51843,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
63458,SRR13839917,SRX10218307,SRS8362893,SRP309041,PRJNA706190,Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling,GSE168131,Transcriptome Analysis,The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS.,parent bioproject:PRJNA706402,pubmed:34936864,,High Wnt NC cells 1,GSM5129517,,tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt,High Wnt NC cells 1,reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample,FACS sorted NC cells,,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,,genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt,GSM5129517,GSM5129517: High Wnt NC cells 1; Danio rerio; RNA Seq,GSM5129517,,1,Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol.,GEO Accession:GSM5129517,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP309041,,loader:fastq load.py,nR032-L4-G1-P010-TAAGGC-READ1-Sequences.txt nR032-L4-G1-P010-TAAGGC-READ2-Sequences.txt,fastq fastq,3745434914.0,18541757.0,GSM5129517 r1,0:101 1:101,A:936339102;C:939766668;G:898475105;T:970783756;N:70283,101,101,,,936339102,939766668,898475105,970783756,70283,SRX10218307,SRS8362893,SRA1202348,GEO,"Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine",2,0.91218,0.92961,0.05044,0.05165,0.75463,0.75373,0.52717,0.52628,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2021-03-03,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
68780,SRR18192263,SRX14338908,SRS12152837,SRP362184,PRJNA812001,scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish,GSE197757,Transcriptome Analysis,In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish  we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion  and then performed scRNA sequencing. These single ECs were isolated at two different time points  21 hpf and 28 hpf  when the lumen of the DA is established and the EHT begins   respectively. Overall design: Spatial photoconversion DA roof versus DA floor  cell dissociation and mannual picking of photoconverted ECs,,pubmed:35333649,,ventral EC 28hpf D12D23 1,GSM5929627,,source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,ventral EC 28hpf D12D23 1,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore  q 20   phred33   stringency 5   length 20  e 0.1   paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trunk DA endothelium,,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,GSM5929627,GSM5929627: ventral EC 28hpf D12D23 1; Danio rerio; RNA Seq,GSM5929627 r1,GSM5929627,1,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP362184,,loader:fastq load.py,M12D23_1_1.fq.gz M12D23_1_2.fq.gz,fastq fastq,3170077200.0,10566924.0,GSM5929627 r1,0:150 1:150,A:895284956;C:687951853;G:714718914;T:872030334;N:91143,150,150,,,895284956,687951853,714718914,872030334,91143,SRX14338908,SRS12152837,,,"Wen's lab, LIFS, HKUST",2,0.86937,0.859,0.06355,0.0627,0.87663,0.87969,0.54768,0.54015,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2022-03-02,Pharyngula,Embryo,Heart,Cardiovascular System
68781,SRR18192264,SRX14338907,SRS12152836,SRP362184,PRJNA812001,scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish,GSE197757,Transcriptome Analysis,In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish  we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion  and then performed scRNA sequencing. These single ECs were isolated at two different time points  21 hpf and 28 hpf  when the lumen of the DA is established and the EHT begins   respectively. Overall design: Spatial photoconversion DA roof versus DA floor  cell dissociation and mannual picking of photoconverted ECs,,pubmed:35333649,,ventral EC 28hpf M12D9 2,GSM5929626,,source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,ventral EC 28hpf M12D9 2,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore  q 20   phred33   stringency 5   length 20  e 0.1   paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trunk DA endothelium,,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,GSM5929626,GSM5929626: ventral EC 28hpf M12D9 2; Danio rerio; RNA Seq,GSM5929626 r1,GSM5929626,1,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP362184,,loader:fastq load.py,M12D9_2_1.fq.gz M12D9_2_2.fq.gz,fastq fastq,2821946100.0,9406487.0,GSM5929626 r1,0:150 1:150,A:833459321;C:543141040;G:577507179;T:867795846;N:42714,150,150,,,833459321,543141040,577507179,867795846,42714,SRX14338907,SRS12152836,,,"Wen's lab, LIFS, HKUST",2,0.73514,0.75198,0.03754,0.03907,0.89838,0.89558,0.47184,0.47431,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2022-03-02,Pharyngula,Embryo,Heart,Cardiovascular System
68782,SRR18192268,SRX14338906,SRS12152835,SRP362184,PRJNA812001,scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish,GSE197757,Transcriptome Analysis,In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish  we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion  and then performed scRNA sequencing. These single ECs were isolated at two different time points  21 hpf and 28 hpf  when the lumen of the DA is established and the EHT begins   respectively. Overall design: Spatial photoconversion DA roof versus DA floor  cell dissociation and mannual picking of photoconverted ECs,,pubmed:35333649,,ventral EC 28hpf M12D24 1,GSM5929625,,source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,ventral EC 28hpf M12D24 1,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore  q 20   phred33   stringency 5   length 20  e 0.1   paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trunk DA endothelium,,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,GSM5929625,GSM5929625: ventral EC 28hpf M12D24 1; Danio rerio; RNA Seq,GSM5929625 r1,GSM5929625,1,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP362184,,loader:fastq load.py,M12D24_1_1.fq.gz M12D24_1_2.fq.gz,fastq fastq,3437508900.0,11458363.0,GSM5929625 r1,0:150 1:150,A:949393206;C:771172192;G:792724386;T:924119993;N:99123,150,150,,,949393206,771172192,792724386,924119993,99123,SRX14338906,SRS12152835,,,"Wen's lab, LIFS, HKUST",2,0.8808,0.87092,0.05011,0.04935,0.89451,0.89593,0.51071,0.5107,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2022-03-02,Pharyngula,Embryo,Heart,Cardiovascular System
68783,SRR18192265,SRX14338905,SRS12152834,SRP362184,PRJNA812001,scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish,GSE197757,Transcriptome Analysis,In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish  we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion  and then performed scRNA sequencing. These single ECs were isolated at two different time points  21 hpf and 28 hpf  when the lumen of the DA is established and the EHT begins   respectively. Overall design: Spatial photoconversion DA roof versus DA floor  cell dissociation and mannual picking of photoconverted ECs,,pubmed:35333649,,ventral EC 28hpf M12D22 7,GSM5929624,,source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,ventral EC 28hpf M12D22 7,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore  q 20   phred33   stringency 5   length 20  e 0.1   paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trunk DA endothelium,,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,GSM5929624,GSM5929624: ventral EC 28hpf M12D22 7; Danio rerio; RNA Seq,GSM5929624 r1,GSM5929624,1,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP362184,,loader:fastq load.py,M12D22_7_1.fq.gz M12D22_7_2.fq.gz,fastq fastq,3353765100.0,11179217.0,GSM5929624 r1,0:150 1:150,A:912815682;C:764078293;G:783280096;T:893499532;N:91497,150,150,,,912815682,764078293,783280096,893499532,91497,SRX14338905,SRS12152834,,,"Wen's lab, LIFS, HKUST",2,0.92895,0.92193,0.06189,0.05719,0.95674,0.95751,0.43458,0.48713,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2022-03-02,Pharyngula,Embryo,Heart,Cardiovascular System
68784,SRR18192266,SRX14338904,SRS12152833,SRP362184,PRJNA812001,scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish,GSE197757,Transcriptome Analysis,In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish  we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion  and then performed scRNA sequencing. These single ECs were isolated at two different time points  21 hpf and 28 hpf  when the lumen of the DA is established and the EHT begins   respectively. Overall design: Spatial photoconversion DA roof versus DA floor  cell dissociation and mannual picking of photoconverted ECs,,pubmed:35333649,,ventral EC 28hpf M12D22 5,GSM5929623,,source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,ventral EC 28hpf M12D22 5,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore  q 20   phred33   stringency 5   length 20  e 0.1   paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trunk DA endothelium,,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,GSM5929623,GSM5929623: ventral EC 28hpf M12D22 5; Danio rerio; RNA Seq,GSM5929623 r1,GSM5929623,1,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP362184,,loader:fastq load.py,M12D22_5_1.fq.gz M12D22_5_2.fq.gz,fastq fastq,2976989100.0,9923297.0,GSM5929623 r1,0:150 1:150,A:827316613;C:664047061;G:674937107;T:810600886;N:87433,150,150,,,827316613,664047061,674937107,810600886,87433,SRX14338904,SRS12152833,,,"Wen's lab, LIFS, HKUST",2,0.93146,0.93345,0.06672,0.0674,0.8788,0.87988,0.5154,0.53867,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2022-03-02,Pharyngula,Embryo,Heart,Cardiovascular System
68785,SRR18192267,SRX14338903,SRS12152832,SRP362184,PRJNA812001,scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish,GSE197757,Transcriptome Analysis,In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish  we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion  and then performed scRNA sequencing. These single ECs were isolated at two different time points  21 hpf and 28 hpf  when the lumen of the DA is established and the EHT begins   respectively. Overall design: Spatial photoconversion DA roof versus DA floor  cell dissociation and mannual picking of photoconverted ECs,,pubmed:35333649,,ventral EC 28hpf M12D2 2,GSM5929622,,source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,ventral EC 28hpf M12D2 2,Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore  q 20   phred33   stringency 5   length 20  e 0.1   paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample,Trunk DA endothelium,,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:28 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs,GSM5929622,GSM5929622: ventral EC 28hpf M12D2 2; Danio rerio; RNA Seq,GSM5929622 r1,GSM5929622,1,Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope  then washed with 2% BSA/PBS  and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP362184,,loader:fastq load.py,M12D2_2_1.fq.gz M12D2_2_2.fq.gz,fastq fastq,3372720300.0,11242401.0,GSM5929622 r1,0:150 1:150,A:988221703;C:669226615;G:703188465;T:1012044907;N:38610,150,150,,,988221703,669226615,703188465,1012044907,38610,SRX14338903,SRS12152832,,,"Wen's lab, LIFS, HKUST",2,0.86571,0.86595,0.0657,0.06575,0.87564,0.87614,0.53669,0.53356,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,sc,single_cell_plate,smartseq,,China,2022-03-02,Pharyngula,Embryo,Heart,Cardiovascular System