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
11240,ERR10782553,ERX10233130,ERS14439195,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 2,E MTAB 12503:Sample 2,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 2 p,Sample 2 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz,fastq fastq,16267571562.0,53866131.0,E MTAB 12503:20170530.A 2 R,0:151 1:151,A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668,151,151,,,4395815325,3765428574,3780844712,4310729283,14753668,ERX10233130,ERS14439195,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.86977,0.8727,0.28497,0.28427,0.70763,0.72301,0.47478,0.47986,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11241,ERR10782552,ERX10233129,ERS14439194,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 1,E MTAB 12503:Sample 1,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 1 p,Sample 1 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz,fastq fastq,15446599662.0,51147681.0,E MTAB 12503:20170530.A 1 R,0:151 1:151,A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332,151,151,,,4289931639,3451135010,3474244788,4217248893,14039332,ERX10233129,ERS14439194,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.90114,0.90507,0.32128,0.32127,0.70232,0.71956,0.47336,0.47528,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11243,ERR10782550,ERX10233127,ERS14439192,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 4,E MTAB 12503:Sample 4,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 4 p,Sample 4 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz,fastq fastq,15697575554.0,51978727.0,E MTAB 12503:20170530.A 4 R,0:151 1:151,A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133,151,151,,,4256444510,3622485921,3650190489,4154211501,14243133,ERX10233127,ERS14439192,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.87714,0.88071,0.29319,0.29235,0.69844,0.7164,0.47594,0.47385,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11244,ERR10782549,ERX10233126,ERS14439191,ERP144048,PRJEB58983,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E-MTAB-12503,Transcriptome Analysis,Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies  concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing  transport  and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here  we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function  we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns  a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling  and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent  early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b  wnt11f2  fzd7a  and vangl2. Following axis formation  rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM  that forms the hematopoietic  cardiovascular  kidney  and forelimb skeleton progenitors. Subsequently  rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a  kdrl  sox7  and the megakaryocyte regulator gfi1aa. Lastly  we document similar hematopoietic defects upon loss of vangl2. Together  our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our findings establish a developmental framework that connects the complex TAR Syndrome phenotypes to a potential LPM origin.,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Sample 3,E MTAB 12503:Sample 3,,strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,,,,,,,,,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,E MTAB 12503:Sample 3 p,Sample 3 p,RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined  pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen  with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina.,Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RANDOM,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP144048,Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling,ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31,20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz,fastq fastq,13839085674.0,45824787.0,E MTAB 12503:20170530.A 3 R,0:151 1:151,A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362,151,151,,,3812423011,3120168590,3163957945,3729983766,12552362,ERX10233126,ERS14439191,ERA20162442,University of Zurich|European Nucleotide Archive,University of Zurich|European Nucleotide Archive,2,0.88987,0.74432,0.33651,0.27875,0.69229,0.72934,0.46981,0.46116,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,sc,unknown,unknown,,Switzerland,2023-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
11753,ERR11758614,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz,fastq fastq,226833768.0,1800268.0,E MTAB 13196:FliTp124hpf S25 L001,0:28 1:98,A:65319978;C:50920193;G:49999849;T:60474280;N:119468,28,98,,,65319978,50920193,49999849,60474280,119468,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00122,0.88236,0.00056,0.09684,0.9978,0.89309,0.424,0.44186,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11754,ERR11758619,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz,fastq fastq,261098334.0,2072209.0,E MTAB 13196:FliTp124hpf S27 L001,0:28 1:98,A:76098436;C:58031830;G:57099955;T:69729759;N:138354,28,98,,,76098436,58031830,57099955,69729759,138354,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00109,0.87641,0.00062,0.0976,0.99837,0.90065,0.45555,0.48712,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11755,ERR11758589,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz,fastq fastq,1168367130.0,9272755.0,E MTAB 13196:FliTp124hpf S16 L005,0:28 1:98,A:323651598;C:269884286;G:268030176;T:306695030;N:106040,28,98,,,323651598,269884286,268030176,306695030,106040,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00491,0.90853,0.00131,0.07851,0.99019,0.84331,0.41536,0.48076,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11756,ERR11758638,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz,fastq fastq,864786636.0,6863386.0,E MTAB 13196:FliTp124hpf S22 L001,0:28 1:98,A:241767760;C:198370882;G:198049093;T:226508751;N:90150,28,98,,,241767760,198370882,198049093,226508751,90150,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00375,0.89002,0.00114,0.0769,0.99237,0.84563,0.41796,0.48995,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11757,ERR11758599,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz,fastq fastq,1795799502.0,14252377.0,E MTAB 13196:FliTp124hpf S15 L005,0:28 1:98,A:500590460;C:413239086;G:410401125;T:471402890;N:165941,28,98,,,500590460,413239086,410401125,471402890,165941,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00492,0.91242,0.0012,0.08044,0.99007,0.84668,0.42778,0.49291,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11758,ERR11758601,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz,fastq fastq,266141358.0,2112233.0,E MTAB 13196:FliTp124hpf S26 L001,0:28 1:98,A:76996100;C:59592346;G:58963461;T:70457732;N:131719,28,98,,,76996100,59592346,58963461,70457732,131719,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00106,0.88422,0.00046,0.09358,0.99782,0.89449,0.47826,0.48948,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11759,ERR11758630,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz,fastq fastq,1812847428.0,14387678.0,E MTAB 13196:FliTp124hpf S14 L005,0:28 1:98,A:502956890;C:417865079;G:416595454;T:475266679;N:163326,28,98,,,502956890,417865079,416595454,475266679,163326,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00483,0.91317,0.00123,0.07918,0.99036,0.84143,0.40704,0.4819,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11760,ERR11758603,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz,fastq fastq,1544281830.0,12256205.0,E MTAB 13196:FliTp124hpf S13 L005,0:28 1:98,A:428008915;C:356252081;G:354333187;T:405545992;N:141655,28,98,,,428008915,356252081,354333187,405545992,141655,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00507,0.91025,0.00138,0.07858,0.98987,0.84295,0.41793,0.4891,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11761,ERR11758613,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz,fastq fastq,761441436.0,6043186.0,E MTAB 13196:FliTp124hpf S21 L001,0:28 1:98,A:212876877;C:174700212;G:174244892;T:199537401;N:82054,28,98,,,212876877,174700212,174244892,199537401,82054,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00334,0.88899,0.00106,0.07762,0.99322,0.84476,0.42792,0.48783,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11762,ERR11758645,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz,fastq fastq,873938772.0,6936022.0,E MTAB 13196:FliTp124hpf S23 L001,0:28 1:98,A:245075115;C:199879929;G:199312177;T:229576663;N:94888,28,98,,,245075115,199879929,199312177,229576663,94888,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00361,0.88671,0.00104,0.07855,0.99255,0.84723,0.41141,0.4885,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11763,ERR11758598,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz,fastq fastq,164465532.0,1305282.0,E MTAB 13196:FliTp124hpf S28 L001,0:28 1:98,A:47319366;C:37063279;G:36394680;T:43602586;N:85621,28,98,,,47319366,37063279,36394680,43602586,85621,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00117,0.88222,0.00058,0.09358,0.99799,0.89217,0.54867,0.48545,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11764,ERR11758593,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz,fastq fastq,558365976.0,4431476.0,E MTAB 13196:FliTp124hpf S24 L001,0:28 1:98,A:156054630;C:128109738;G:127885708;T:146256146;N:59754,28,98,,,156054630,128109738,127885708,146256146,59754,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00345,0.8879,0.00104,0.07718,0.99322,0.84364,0.38266,0.49193,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11765,ERR11758635,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz,fastq fastq,1144014102.0,9079477.0,E MTAB 13196:Etv2Kaede WT S6 L001,0:28 1:98,A:316366230;C:260322813;G:259447166;T:307680623;N:197270,28,98,,,316366230,260322813,259447166,307680623,197270,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00336,0.89267,0.00137,0.13734,0.99545,0.81957,0.3734,0.53458,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11766,ERR11758622,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz,fastq fastq,919270926.0,7295801.0,E MTAB 13196:Etv2Kaede WT S8 L001,0:28 1:98,A:259787542;C:207541571;G:206711907;T:245072713;N:157193,28,98,,,259787542,207541571,206711907,245072713,157193,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00358,0.88757,0.00137,0.15368,0.99551,0.83378,0.36405,0.53733,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11767,ERR11758644,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz,fastq fastq,877658166.0,6965541.0,E MTAB 13196:Etv2Kaede WT S5 L001,0:28 1:98,A:243057461;C:199464116;G:198654377;T:236322700;N:159512,28,98,,,243057461,199464116,198654377,236322700,159512,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00328,0.88916,0.00127,0.13782,0.99559,0.81925,0.38227,0.53623,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11768,ERR11758628,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz,fastq fastq,930443598.0,7384473.0,E MTAB 13196:Etv2Kaede WT S7 L001,0:28 1:98,A:258539610;C:211017108;G:209074684;T:251641766;N:170430,28,98,,,258539610,211017108,209074684,251641766,170430,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00355,0.88938,0.00148,0.14297,0.99569,0.83358,0.35626,0.53314,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25127,SRR25610724,SRX21337840,SRS18583009,SRP454647,PRJNA1004574,Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf,GSE240655,Transcriptome Analysis,Melanocytes of the skin have traditionally been viewed as a homogeneous population  however  recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further  we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study  we utilized a transgenic zebrafish line  Tgmifa:GFP  that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter  mitfa  labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer,parent bioproject:PRJNA975369,pubmed:39163475,,mitfa high  zf  scRNAseq,GSM7706847,,tissue:mitfa:GFP+ cells|genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP high|age:24 hpf loc name:missing|collection date:missing,mitfa high  zf  scRNAseq,The demultiplexing  barcode processing  gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,mitfa:GFP+ cells,,Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter’s instructions single cell 3’ v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.,,genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP high|age:24 hpf,GSM7706847,GSM7706847: mitfa high  zf  scRNAseq; Danio rerio; RNA Seq,GSM7706847 r1,GSM7706847,1,Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP454647,,loader:fastq load.py,HM_S4_L001_I1_001.fastq.gz HM_S4_L001_R1_001.fastq.gz HM_S4_L001_R2_001.fastq.gz,fastq fastq fastq,24842565758.0,195610754.0,GSM7706847 r1,0:8 1:28 2:91,A:5175410152;C:3650416721;G:4658958024;T:4315769305;N:24412,8,28,91,,5175410152,3650416721,4658958024,4315769305,24412,SRX21337840,SRS18583009,SRA1691286,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",1,0.84133,,0.13672,,0.84756,,0.52135,,91,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,India,2023-08-11,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25128,SRR25610725,SRX21337839,SRS18583008,SRP454647,PRJNA1004574,Gene expression profile at single cell level of mitfa:GFP labelled zebrafish cells at 24hpf,GSE240655,Transcriptome Analysis,Melanocytes of the skin have traditionally been viewed as a homogeneous population  however  recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further  we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study  we utilized a transgenic zebrafish line  Tgmifa:GFP  that expresses green fluorescent protein GFP under the control of a melanocyte specific promoter  mitfa  labelling only those cells in which mitfa promoter is active. We then performed single cell RNA sequencing scRNA seq analysis to explore the diversity of mitfa:GFP positive cells. Overall design: Tgmitfa:GFP zebrafish embryos were raised till 24 hpf and then the cells were isolated. The cells expressing mitfa:GFP were then sorted into low and high GFP population using a flow cytometer,parent bioproject:PRJNA975369,pubmed:39163475,,mitfa low  zf  scRNAseq,GSM7706846,,tissue:mitfa:GFP+ cells|genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP low|age:24 hpf loc name:missing|collection date:missing,mitfa low  zf  scRNAseq,The demultiplexing  barcode processing  gene counting and aggregation were done using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,mitfa:GFP+ cells,,Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter’s instructions single cell 3’ v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.,,genotype:Tgmitfa:GFP|cell type:mitfa:GFP+ cells|population:mitfa:GFP low|age:24 hpf,GSM7706846,GSM7706846: mitfa low  zf  scRNAseq; Danio rerio; RNA Seq,GSM7706846 r1,GSM7706846,1,Tgmitfa:GFP zebrafish embryos at 24hpf were dechorinated using 5 mg/ml pronase for 10 15 min  deyolked in Ringer's solution ice cold using a micropipette tip and spun at 100 g for 2 min at 4°C . The embryo bodies were trypsinized using TrypLE Express for 15 or 30 min at room temperature  post discarding the supernatent. Clumps were removed by passing the cells through a 70 μm cell strainer and washing twice with ice cold phosphate buffered saline. The cells expressing low and high levels of mitfa:GFP were then sorted using a flow cytometer and taken for library preparation. Libraries was prepared according to the manufacter's instructions single cell three prime v3.1 single index protocol  10x Genomics. Briefly  24hpf mitfa:GFP low and high zebrafish cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP454647,,loader:fastq load.py,LM_S3_L001_R2_001.fastq.gz LM_S3_L001_R1_001.fastq.gz LM_S3_L001_I1_001.fastq.gz,fastq fastq fastq,17519211850.0,137946550.0,GSM7706846 r1,0:8 1:28 2:91,A:3674575574;C:2564940740;G:3313017210;T:3000585838;N:16688,8,28,91,,3674575574,2564940740,3313017210,3000585838,16688,SRX21337839,SRS18583008,SRA1691286,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",1,0.81163,,0.13698,,0.859,,0.52032,,91,,B,,usable mapping rate,illumina,nextseq_v2,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,India,2023-08-11,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25129,SRR25619749,SRX21346683,SRS18591743,SRP454714,PRJNA1004663,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival,GSE240721,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,GSM7708237,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM7708237,GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq,GSM7708237 r1,GSM7708237,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454714,,loader:fastq load.py,CEL201106AN_WT-2_S20_L004_R2_001.fastq.gz CEL201106AN_WT-2_S20_L004_R1_001.fastq.gz CEL201106AN_WT-2_S20_L004_I1_001.fastq.gz,fastq fastq fastq,17931740743.0,141194809.0,GSM7708237 r1,0:8 1:28 2:91,A:3982504087;C:2545259636;G:2793618614;T:3526744725;N:600557,8,28,91,,3982504087,2545259636,2793618614,3526744725,600557,SRX21346683,SRS18591743,SRA1691311,Oregon Health and Science Univ,Oregon Health and Science Univ,1,0.87401,,0.26924,,0.7517,,0.5102,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-11,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25130,SRR25619750,SRX21346683,SRS18591743,SRP454714,PRJNA1004663,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival,GSE240721,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,GSM7708237,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM7708237,GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq,GSM7708237 r1,GSM7708237,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454714,,loader:fastq load.py,CEL201106AN_WT-2_S19_L004_I1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R1_001.fastq.gz CEL201106AN_WT-2_S19_L004_R2_001.fastq.gz,fastq fastq fastq,15740158766.0,123938258.0,GSM7708237 r2,0:8 1:28 2:91,A:3499017196;C:2231848518;G:2450171440;T:3096822046;N:522278,8,28,91,,3499017196,2231848518,2450171440,3096822046,522278,SRX21346683,SRS18591743,SRA1691311,Oregon Health and Science Univ,Oregon Health and Science Univ,1,0.87457,,0.27073,,0.75278,,0.50801,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-11,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25131,SRR25619751,SRX21346683,SRS18591743,SRP454714,PRJNA1004663,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival,GSE240721,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,GSM7708237,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM7708237,GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq,GSM7708237 r1,GSM7708237,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454714,,loader:fastq load.py,CEL201106AN_WT-2_S18_L004_R2_001.fastq.gz CEL201106AN_WT-2_S18_L004_R1_001.fastq.gz CEL201106AN_WT-2_S18_L004_I1_001.fastq.gz,fastq fastq fastq,14146022254.0,111386002.0,GSM7708237 r3,0:8 1:28 2:91,A:3147384451;C:2003642594;G:2200506573;T:2784120122;N:472442,8,28,91,,3147384451,2003642594,2200506573,2784120122,472442,SRX21346683,SRS18591743,SRA1691311,Oregon Health and Science Univ,Oregon Health and Science Univ,1,0.873,,0.27005,,0.75122,,0.5172,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-11,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25132,SRR25619752,SRX21346683,SRS18591743,SRP454714,PRJNA1004663,Single cell analysis of Rohon Beard neurons implicates Fgf signaling in axon maintenance and cell survival,GSE240721,Other,Peripheral sensory neurons are a critical part of the nervous system that transmit a multitude of sensory stimuli to the central nervous system. During larval and juvenile stages in zebrafish  this function is mediated by Rohon Beard somatosensory neurons RBs. RBs are optically accessible and amenable to experimental manipulation  making them a powerful system for mechanistic investigation of sensory neurons. Previous studies provided evidence that RBs fall into multiple subclasses; however  the number and molecular make up of these potential RB subtypes have not been well defined. Using a single cell RNA sequencing scRNA seq approach  we demonstrate that larval RBs in zebrafish fall into three  largely non overlapping classes of neurons. We also show that RBs are molecularly distinct from trigeminal neurons in zebrafish. Cross species transcriptional analysis indicates that one RB subclass is similar to a mammalian group of A fiber sensory neurons. Another RB subclass is predicted to sense multiple modalities  including mechanical stimulation and chemical irritants. We leveraged our scRNA seq data to determine that the fibroblast growth factor Fgf pathway is active in RBs. Pharmacological and genetic inhibition of this pathway led to defects in axon maintenance and RB cell death. Moreover  this phenotype can be phenocopied by treatment with an FDA approved Fgf inhibitor dovitinib  which is used in clinic and causes peripheral neuropathy. Importantly  dovitinib mediated axon loss can be suppressed by loss of Sarm1  a positive regulator of neuronal cell death and axonal injury. This offers a molecular target for future clinical intervention to fight neurotoxic effects of this drug. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,GSM7708237,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM7708237,GSM7708237: 30 hpf TgBACneurod1:EGFPnl1 zebrafish embryos  scRNAseq; Danio rerio; RNA Seq,GSM7708237 r1,GSM7708237,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454714,,loader:fastq load.py,CEL201106AN_WT-2_S17_L004_I1_001.fastq.gz CEL201106AN_WT-2_S17_L004_R1_001.fastq.gz CEL201106AN_WT-2_S17_L004_R2_001.fastq.gz,fastq fastq fastq,14874414752.0,117121376.0,GSM7708237 r4,0:8 1:28 2:91,A:3301539475;C:2111151786;G:2317995421;T:2926865071;N:493463,8,28,91,,3301539475,2111151786,2317995421,2926865071,493463,SRX21346683,SRS18591743,SRA1691311,Oregon Health and Science Univ,Oregon Health and Science Univ,1,0.87465,,0.26977,,0.75211,,0.51651,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-08-11,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
25133,SRR25634296,SRX21361065,SRS18605555,SRP454944,PRJNA1005241,Nkx2.7 is a Conserved Regulator of Craniofacial Development,GSE240780,Transcriptome Analysis,Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.,,pubmed:40268889,,KC002  scRNAseq,GSM7709162,,source name:Pharyngeal arches|genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing,KC002  scRNAseq,The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files,Pharyngeal arches,,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,genotype:nkx2.7 / |tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf,GSM7709162,GSM7709162: KC002  scRNAseq; Danio rerio; RNA Seq,GSM7709162 r1,GSM7709162,1,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454944,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC002 S1 L004 I1 001.fastq.gz   read2PairFiles=KC002 S1 L004 I2 001.fastq.gz   read3PairFiles=KC002 S1 L004 R1 001.fastq.gz   read4PairFiles=KC002 S1 L004 R2 001.fastq.gz,KC002_S1_L004_I1_001.fastq.gz KC002_S1_L004_I2_001.fastq.gz KC002_S1_L004_R1_001.fastq.gz KC002_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,65825988564.0,296513462.0,GSM7709162 r1,0:10 1:10 2:101 3:101,A:14990994149;C:11485312838;G:11921291570;T:21497933732;N:187035,10,10,101,101,14990994149,11485312838,11921291570,21497933732,187035,SRX21361065,SRS18605555,SRA1692494,"SangesLab Computational Genomics, NEUROSCIENCE, SISSA","SangesLab Computational Genomics, NEUROSCIENCE, SISSA",2,0.00059,0.93473,2e-05,0.14487,0.99949,0.78364,0.5,0.52799,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Italy,2023-08-14,Pharyngula,Embryo,Pharyngeal Arch,Multi-system
25134,SRR25634297,SRX21361064,SRS18605556,SRP454944,PRJNA1005241,Nkx2.7 is a Conserved Regulator of Craniofacial Development,GSE240780,Transcriptome Analysis,Pharyngeal arch cells are comprised of endoderm  mesoderm  and neural crest layers. We used single cell RNA sequencing scRNA seq to analyze the genetic differences in pharyngeal arch cell types between wild type and nkx2.7 /  samples. Overall design: Pharyngeal arch cells were obtained through manual dissection of wild type and nkx2.7 /  embryos at 26 hpf. All embryos were positive for TgBACtcf21:mcherry NTR  which was used as a visual guide for dissection. Cells were FACS sorted to eliminate dead cells from sequencing. 2 wild type embryos and 2 nkx2.7 /  samples were pooled for submission.,,pubmed:40268889,,KC001  scRNAseq,GSM7709161,,source name:Pharyngeal arches|genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf|geo loc name:missing|collection date:missing,KC001  scRNAseq,The read alignment and gene counting were made using the Cell Ranger software v6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 version 105 Supplementary files format and content: Tab separated values files and matrix files,Pharyngeal arches,,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,genotype:wild type|tissue:Pharyngeal arches|strain:AB|developmental stage:26 hpf,GSM7709161,GSM7709161: KC001  scRNAseq; Danio rerio; RNA Seq,GSM7709161 r1,GSM7709161,1,From the offspring of an intercross of nkx2.7+/ ;Tgtcf21:NTRO mCherrypd108  two wild type and two nkx2.7 /  embryos were identified by genotyping.  The pharyngeal arches and surrounding tissue were dissected  dissociated  and submitted for flow cytometry.  Cellular dissociation was performed with liberase solution in PBS at 28°C with pipetting every five minutes until adequately homogenized in solution.  Fetal Bovine Serum FBS 5% of volume was then added to each sample to arrest the dissociation and each sample was centrifuged at 4°C.  The excess supernatant was removed and the pellet was resuspended in PBS/1% FBS and filtered through a 40 m cell strainer.  Finally  DAPI and DRAQ5 were added and cells were sorted using a SORP FACSAriaTM Cell Sorter BD Biosciences under gentle conditions with the 130 μm nozzle at 12 PSI.  NERL Diluent 2 Thermo Fisher  DIL5522 solution was used for sheath fluid.  The FACSAria was calibrated per the standard protocol in the CSCI Flow Cytometry Core Facility using Cytometer Setup and Tracking Beads BD Biosciences  655051  SPHERO Rainbow Calibration Particles 8 Peaks 3.0 m  5 mL Spherotech  RCP 30 5A  followed by optimization of the drop charge delay using BD FACS Accudrop Beads BD Biosciences  345249. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454944,,loader:fastq load.py|options:  readTypes=TTBB   read1PairFiles=KC001 S1 L004 I1 001.fastq.gz   read2PairFiles=KC001 S1 L004 I2 001.fastq.gz   read3PairFiles=KC001 S1 L004 R1 001.fastq.gz   read4PairFiles=KC001 S1 L004 R2 001.fastq.gz,KC001_S1_L004_I1_001.fastq.gz KC001_S1_L004_I2_001.fastq.gz KC001_S1_L004_R1_001.fastq.gz KC001_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,69380677872.0,312525576.0,GSM7709161 r1,0:10 1:10 2:101 3:101,A:16018222868;C:11704492905;G:12161620273;T:23245625739;N:204567,10,10,101,101,16018222868,11704492905,12161620273,23245625739,204567,SRX21361064,SRS18605556,SRA1692494,"SangesLab Computational Genomics, NEUROSCIENCE, SISSA","SangesLab Computational Genomics, NEUROSCIENCE, SISSA",2,0.00071,0.93976,0.0001,0.12725,0.99945,0.78457,0.75,0.50121,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Italy,2023-08-14,Pharyngula,Embryo,Pharyngeal Arch,Multi-system
31527,SRR28419475,SRX24023798,SRS20818154,SRP497235,PRJNA1090867,Single cell RNA seq of zebrafish endothelial cells,GSE262232,Transcriptome Analysis,We performed single cell RNA sequencing scRNA seq for isolated endothelial cells Overall design: Tgkdrl:EGFP zebrafish embryos were digested into single cell suspension  EGFP positive cells were isolated using FACS and subjected to 10X Genomics Chromium scRNAseq.,,pubmed:39977018,,Zebrafish endothelial cells 34 hpf,GSM8160885,,source name:Whole body|tissue:Whole body|age:embryo|geo loc name:missing|collection date:missing,Zebrafish endothelial cells 34 hpf,Cell Ranger v2.1 was used to de multiplex raw base call BCL files generated by Illumina sequencers into FASTQ files  perform the alignment  barcode counting  and UMI counting. Assembly: GRCz11 Supplementary files format and content: Tab seprated values files,Whole body,,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer’s protocol.,,tissue:Whole body|age:embryo,GSM8160885,GSM8160885: Zebrafish endothelial cells 34 hpf; Danio rerio; RNA Seq,GSM8160885 r1,GSM8160885,1,Whole Tgkdrl:EGFP zebrafish embryos were digested into single cell suspensions  EGFP positive cells were isolated using FACS Single cell suspension was loaded into the 10X Chromium system and cDNA libraries were constructed using Chromium Next GEM Single Cell 3′ GEM  Library and Gel Bead Kit v2 10X Genomics according to manufacturer's protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP497235,,assembly:GRCz11|intentional duplicate|dangling references:treat as unmapped|dangling references:skip reference resolution,34hpf_possorted_genome_bam.bam,10X Genomics bam file,8518745844.0,86925978.0,GSM8160885 r1,0:98,A:2440648674;C:1828442217;G:2000096456;T:2232243146;N:17315351,98,,,,2440648674,1828442217,2000096456,2232243146,17315351,SRX24023798,SRS20818154,SRA1835509,Uppsala University,Uppsala University,1,0.92268,,0.1011,,0.82235,,0.50276,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-03-22,Pharyngula,Embryo,Trunk,Surface Structure
31972,SRR28854385,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S4_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S4_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S4_L001_R2_001.fastq.gz,fastq fastq fastq,5724917176.0,45078088.0,GSM8244692 r1,0:8 1:28 2:91,A:1233470398;C:840754101;G:925102747;T:1102656199;N:122563,8,28,91,,1233470398,840754101,925102747,1102656199,122563,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31973,SRR28854386,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S4_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S4_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S4_L002_R2_001.fastq.gz,fastq fastq fastq,5783895468.0,45542484.0,GSM8244692 r2,0:8 1:28 2:91,A:1245735118;C:849017838;G:935656364;T:1113856043;N:100681,8,28,91,,1245735118,849017838,935656364,1113856043,100681,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31974,SRR28854387,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S3_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S3_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S3_L001_R2_001.fastq.gz,fastq fastq fastq,6548658861.0,51564243.0,GSM8244692 r3,0:8 1:28 2:91,A:1411724640;C:961558289;G:1057832581;T:1261091330;N:139273,8,28,91,,1411724640,961558289,1057832581,1261091330,139273,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31975,SRR28854388,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S3_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S3_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S3_L002_R2_001.fastq.gz,fastq fastq fastq,6602135640.0,51985320.0,GSM8244692 r4,0:8 1:28 2:91,A:1422617276;C:968975306;G:1067723068;T:1271232295;N:116175,8,28,91,,1422617276,968975306,1067723068,1271232295,116175,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31976,SRR28854389,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S2_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S2_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S2_L001_R2_001.fastq.gz,fastq fastq fastq,5207105156.0,41000828.0,GSM8244692 r5,0:8 1:28 2:91,A:1121297258;C:765571677;G:841433529;T:1002663097;N:109787,8,28,91,,1121297258,765571677,841433529,1002663097,109787,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31977,SRR28854390,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S2_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S2_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S2_L002_R2_001.fastq.gz,fastq fastq fastq,5257051208.0,41394104.0,GSM8244692 r6,0:8 1:28 2:91,A:1131659183;C:772616863;G:850242289;T:1012253749;N:91380,8,28,91,,1131659183,772616863,850242289,1012253749,91380,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31978,SRR28854391,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S1_L001_I1_001.fastq.gz CEL200616AN_WT_30h_S1_L001_R1_001.fastq.gz CEL200616AN_WT_30h_S1_L001_R2_001.fastq.gz,fastq fastq fastq,5671346544.0,44656272.0,GSM8244692 r7,0:8 1:28 2:91,A:1221772454;C:832992882;G:915744544;T:1093089728;N:121144,8,28,91,,1221772454,832992882,915744544,1093089728,121144,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
31979,SRR28854392,SRX24414680,SRS21169984,SRP505049,PRJNA1106549,Pioneer neurons are molecularly distinct  and their axon targeting is regulated by retinoic acid signaling WT 30 h,GSE266312,Other,During nervous system development  pioneer neurons are the first to extend their axons into target tissues  creating a scaffold for follower neurons. Despite years of study  whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line pLL sensory neurons during axon growth using single cell RNA sequencing scRNA seq revealed that pioneer and follower neurons are transcriptionally distinct. Expression profiling of differentiating pLL progenitors defined follower as the ground state  whereas “pioneer” is a later developmental state. The scRNA seq data revealed active retinoic acid RA signaling in followers  but not in pioneers. Modulation of RA signaling within single pLL neurons showed that its downregulation in pioneers is necessary for expression of neurotrophic factor receptor ret  which is required for correct targeting of pioneer axons. Our study provided insights into the molecular landscape of pioneer neurons and revealed the regulatory role of RA signaling in their development. Overall design: Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 µl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 µm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 µl PBS/ 2% BSA in a siliconized 1.5mL tube.,,,,scRNAseq,GSM8244692,,source name:zebrafish embryo|cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf loc name:missing|collection date:missing,scRNAseq,using Cell Ranger version 3.1.0; 10X Genomics  Pleasanton  CA. USA Assembly: ZebraFishGRCz11 Supplementary files format and content: Tab separated values files and matrix files,zebrafish embryo,,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer’s solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer’s solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter’s instructions single cell 3’ v3 protocol  10x Genomics.,,cell type:neuron|tissue:zebrafish embryo|strain:mixed|age:30 hpf,GSM8244692,GSM8244692: scRNAseq; Danio rerio; RNA Seq,GSM8244692 r1,GSM8244692,1,Thirty hpf TgBACneurod1:EGFPnl1 zebrafish embryos were collected and euthanized in 1.7 ml microcentrifuge tubes. Embryos were deyolked using a calcium free Ringer's solution 116 mM NaCl  2.6 mM KCl  5 mM HEPES pH 7.0  by gently pipetting up and down with a P200 pipet. Embryos were incubated for 5 minutes in Ringer's solution. Embryos were transferred to pre warmed protease solutions 0.25% trypsin  1 mM EDTA  pH 8.0  PBS and collagenase P/HBSS 100 mg/mL was added. Embryos were incubated at 28° C for 15 minutes and were homogenized every 5 minutes using a P1000 pipet. The Stop solution 6X  30% calf serum  6 mM CaCl2  PBS was added and samples were centrifuged 350xg  4° C for 5 minutes. Supernatant was removed and 1 mL of chilled suspension solution was added 1% FBS  0.8 mM CaCl2  50 U/mL penicillin  0.05 mg/mL streptomycin  DMEM. Samples were centrifuged again 350g  4° C for 5 minutes and supernatant was removed. 700 μl of chilled suspension solution was added and cells were resuspended by pipetting. Cells were passed through a 40 μm cell strainer into a FACs tube and kept on ice. GFP and RFP+ cells were FAC sorted on a BD Symphony cell sorter into sorting buffer 50 μl PBS/ 2% BSA in a siliconized 1.5mL tube. Library was performed according to the manufacter's instructions single cell three prime v3 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP505049,,loader:fastq load.py,CEL200616AN_WT_30h_S1_L002_I1_001.fastq.gz CEL200616AN_WT_30h_S1_L002_R1_001.fastq.gz CEL200616AN_WT_30h_S1_L002_R2_001.fastq.gz,fastq fastq fastq,5728522071.0,45106473.0,GSM8244692 r8,0:8 1:28 2:91,A:1233691562;C:840924973;G:926085790;T:1103887111;N:99607,8,28,91,,1233691562,840924973,926085790,1103887111,99607,SRX24414680,SRS21169984,SRA1856329,Oregon Health and Science Univ,Oregon Health and Science Univ,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-04-30,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
33617,SRR30274406,SRX25735496,SRS22375280,SRP526857,PRJNA1148965,The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development,GSE275013,Transcriptome Analysis,Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes  but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question  we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 /  embryos. Loss of Gq/11 activity fully recapitulated the edn1 /  phenotype  with genes encoding for G11 being most essential. Furthermore  inducing Gq activity in edn1 /  embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16   36 hpf. Then  cranial neural crest cells NCCs labeled with two transgenes  sox10:mRFP and fli1a:EGFP  were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.,,pubmed:39345358;pubmed:40171762,,cranial NCCs  YM,GSM8464445,,source name:Facial mesenchyme|tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:YM|geo loc name:missing|collection date:missing,cranial NCCs  YM,Sequence reads were  converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Facial mesenchyme,Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf,Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer’s solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz’s L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics,,tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:YM,GSM8464445,GSM8464445: cranial NCCs  YM; Danio rerio; RNA Seq,GSM8464445 r1,GSM8464445,1,Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz's L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP526857,,,YM-treated_S9_L001_R2_001.fastq.gz YM-treated_S9_L001_R1_001.fastq.gz,fastq fastq,133560759038.0,442254169.0,GSM8464445 r1,0:151 1:151,A:49523643076;C:22144256343;G:30982866215;T:30893839980;N:16153424,151,151,,,49523643076,22144256343,30982866215,30893839980,16153424,SRX25735496,SRS22375280,SRA1949431,"David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus","David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus",2,0.00156,0.3917,0.00133,0.06002,0.99997,0.9529,0.0,0.52259,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-08-16,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
33618,SRR30274407,SRX25735495,SRS22375277,SRP526857,PRJNA1148965,The Gq/11 family of G alpha subunits is necessary and sufficient for lower jaw development,GSE275013,Transcriptome Analysis,Development of the vertebrate jaw apparatus depends on highly conserved signaling pathways. Patterning of the lower jaw is driven by Endothelin receptor type A Ednra and secreted ligand Endothelin 1 Edn1. The Ednra signaling pathway establishes the identity of lower jaw progenitors by regulating expression of numerous patterning genes  but the intracellular signaling mechanisms linking receptor activation to gene regulation remains poorly understood. As a first step towards addressing this question  we examined the function of the Gq/11 family of Ga subunits in zebrafish using pharmacological and genetic ablation of Gq/11 activity and transgenic induction of a constitutively active Gq protein in edn1 /  embryos. Loss of Gq/11 activity fully recapitulated the edn1 /  phenotype  with genes encoding for G11 being most essential. Furthermore  inducing Gq activity in edn1 /  embryos not only restored Ednra dependent jaw structures and gene expression signatures but also caused homeosis of the upper jaw structures into a lower jaw like structure. These results indicate that Gq/11 is necessary and sufficient to mediate the lower jaw patterning mechanism for Ednra. Overall design: Zebrafish embryos were first treated with YM 254890 or DMSO control between 16   36 hpf. Then  cranial neural crest cells NCCs labeled with two transgenes  sox10:mRFP and fli1a:EGFP  were isolated at 36 hpf by fluorescence activated cell sorting FACS. Isolated cranial NCCs were then analyzed by scRNA seq.,,pubmed:39345358;pubmed:40171762,,cranial NCCs  DMSO,GSM8464444,,source name:Facial mesenchyme|tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:DMSO|geo loc name:missing|collection date:missing,cranial NCCs  DMSO,Sequence reads were  converted to count matrices with Cell Ranger v5.0.1 10X Genomics. Subsequent analyses of count matrices were performed with Seurat version 4.3.0 in R studio. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,Facial mesenchyme,Dechorionated zebrafish embryos were treated with 100uM YM 254890 or 10%v/v DMSO vehicle control from 16 hpf 36 hpf,Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer’s solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz’s L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics,,tissue:Facial mesenchyme|age:36 hpf|cell type:Cranial neural crest cells|genotype:Tgsox10:mRFP;Tgfli1a:EGFP|treatment:DMSO,GSM8464444,GSM8464444: cranial NCCs  DMSO; Danio rerio; RNA Seq,GSM8464444 r1,GSM8464444,1,Cranial neural crest cells were isolated from zebrafish embryos using a fli1a:EGFP and sox10:mRFP double labeling technique as described in Barske et al.  2016; Askary et al.  2017; Mitchell et al.  2021 with some modifications. In brief  140 double positive embryos were dechorionated at 14 hpf with 2 mg/ml Pronase Roche  cat. 10165921001  then 70 embryos were treated with 100 uM YM 254890 Adipogen  cat. AG CN2 0509 M001 or DMSO control from 16 hpf 36 hpf. At 36 hpf  10 embryos from each condition were set aside for skeletal preparations at 6 dpf. For the remaining embryos  the heads were severed  pooled  and deyolked by gentle pipetting in Ca2+ free Ringer's solution 116 mM NaCl  2.9 mM KCl  5 mM HEPES  pH 7.0. The embryos were then dissociated into single cells with mechanical agitation and enzymatic digestion for 15 minutes at 4˚C with cold activated protease from Bacillus licheniformis Sigma Aldrich  cat. P5380 in dissociation buffer 10 mg/ml Bacillus licheniformis protease  125 U/ml DNAse  2.5 mM EDTA  PBS  followed by enzyme neutralization with stop solution 30% fetal bovine serum  0.8 mM CaCl2  in PBS. Cells were then centrifuged 400xg  resuspended in cell suspension buffer [1% fetal bovine serum  0.8 mM CaCl2  Leibovitz's L 15 Medium Gibco  cat. 21083 027]  filtered through a 70 uM strainer PluriSelect  cat. 43 10040 40  centrifuged 400xg again and resuspended in sorting buffer 1% fetal bovine serum  1 mM EDTA  25 mM HEPES. EGFP and mRFP double positive cells were then purified with fluorescence activated cell sorting using MoFlo XDP100 Beckman Coulter. A total of 72 000 and 86 000 double positive cells were purified for DMSO and YM treated samples  respectively. Cells were once again centrifuged 400xg and resuspended in cell suspension buffer. post confirming cell viability with trypan blue Gibco  cat. 15250 061  8000 cells for each condition were submitted to the Genomics and Microarray Core CU AMC for single cell RNA sequencing. Library was prepared according to manufacturer's protocol three prime NextGEM V3.1  10X Genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP526857,,,untreated_S8_L001_R2_001.fastq.gz untreated_S8_L001_R1_001.fastq.gz,fastq fastq,105068673228.0,347909514.0,GSM8464444 r1,0:151 1:151,A:37833743112;C:17968955370;G:25241339852;T:24012078661;N:12556233,151,151,,,37833743112,17968955370,25241339852,24012078661,12556233,SRX25735495,SRS22375277,SRA1949431,"David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus","David Clouthier, Craniofacial Biology, University of Colorado Anschutz Medical Campus",2,0.00043,0.49133,0.00042,0.07262,1.0,0.95179,,0.5212,151,151,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-08-16,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
33892,SRR30866052,SRX26263961,SRS22803217,SRP536276,PRJNA1168147,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq],GSE278654,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development  we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.,,,,m4b mut,GSM8552316,,tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No|geo loc name:missing|collection date:missing,m4b mut,Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features  and matrix files,melanocytes,,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,cell type:melanocytes|age:36 hpf|genotype:mgat4b mutant|treatment:No,GSM8552316,GSM8552316: m4b mut; Danio rerio; RNA Seq,GSM8552316 r1,GSM8552316,1,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536276,,loader:fastq load.py,m4b_mut_S2_L001_I1_001.fastq.gz m4b_mut_S2_L001_I2_001.fastq.gz m4b_mut_S2_L001_R1_001.fastq.gz m4b_mut_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,18274385040.0,132423080.0,GSM8552316 r1,0:10 1:10 2:28 3:90,A:3788703303;C:2355223955;G:2645521958;T:3126630009;N:1997975,10,10,28,90,3788703303,2355223955,2645521958,3126630009,1997975,SRX26263961,SRS22803217,SRA1984944,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,India,2024-10-02,Pharyngula,Embryo,Skin,Surface Structure
33893,SRR30866053,SRX26263960,SRS22803216,SRP536276,PRJNA1168147,Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [scRNA seq],GSE278654,Transcriptome Analysis,Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To understand how selective N glycosylation modification performed by mgat4b promote melanocyte development  we performed single cell RNA sequencing of mitfa+ve melanophores sorted from the 36hpf staged zebrafish.,,,,Control,GSM8552315,,tissue:melanocytes|cell type:melanocytes|age:36 hpf|genotype:control|treatment:No|geo loc name:missing|collection date:missing,Control,Cellranger mkfastq pipeline was used to generate fastq files The fastq files were then aligned with custom zebrafish reference assembly GRCz11 using cellranger. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including barcodes and features  and matrix files,melanocytes,,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,cell type:melanocytes|age:36 hpf|genotype:control|treatment:No,GSM8552315,GSM8552315: Control; Danio rerio; RNA Seq,GSM8552315 r1,GSM8552315,1,The gfp positive cells are isolated using FACS and 10x Genomics Next GEM three primereagent kit Dual Index was used for bead generation and cDNA synthesis 10x Genomics Next GEM three primereagent kit Dual Index was used for library construction,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536276,,loader:fastq load.py,con_S1_L001_I1_001.fastq.gz con_S1_L001_I2_001.fastq.gz con_S1_L001_R1_001.fastq.gz con_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,15825218034.0,114675493.0,GSM8552315 r1,0:10 1:10 2:28 3:90,A:3074750870;C:2137365424;G:2401965854;T:2704984993;N:1727229,10,10,28,90,3074750870,2137365424,2401965854,2704984993,1727229,SRX26263960,SRS22803216,SRA1984944,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,India,2024-10-02,Pharyngula,Embryo,Skin,Surface Structure
35387,SRR32649450,SRX27953869,SRS24319773,SRP569567,PRJNA1234533,Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb,GSE291626,Transcriptome Analysis,To understand how neural circuits are assembled  it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family  pcdh7b and pcdh11  are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus  but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast  two members of the delta2 protocadherin family  pcdh10b and pcdh17  are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus  while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36  48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.,,,,OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish,GSM8838716,,source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing,OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish,Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.,Olfactory Sensory Tissue,,10X Genomics V3.3,,tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP,GSM8838716,GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq,GSM8838716 r1,GSM8838716,1,10X Genomics V3.3,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP569567,,loader:fastq load.py,97366_S7_L001_I1_001.fastq.gz 97366_S7_L001_R1_001.fastq.gz 97366_S7_L001_R2_001.fastq.gz,fastq fastq fastq,5962313630.0,45863951.0,GSM8838716 r1,0:8 1:28 2:94,A:1285269727;C:856096209;G:931439088;T:1238303640;N:102730,8,28,94,,1285269727,856096209,931439088,1238303640,102730,SRX27953869,SRS24319773,SRA2091725,"Department of Neuroscience, University of Pennsylvania","Department of Neuroscience, University of Pennsylvania",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-11,Pharyngula,Embryo,Brain,Nervous System
35388,SRR32649451,SRX27953869,SRS24319773,SRP569567,PRJNA1234533,Delta family protocadhins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb,GSE291626,Transcriptome Analysis,To understand how neural circuits are assembled  it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single cell RNA sequencing of olfactory sensory neurons from zebrafish to identify candidate axonal guidance related genes that are differentially expressed according to sensory axon target location in the olfactory bulb. Among the candidates we identified were several members of the non clustered delta protocadherin family of adhesion molecules. We found that two members of the delta1 protocadherin family  pcdh7b and pcdh11  are most highly expressed in sensory neurons that project to the DZ protoglomerulus. Knocking down either one impairs the ability of sensory axons to terminate within the DZ protoglomerulus  but does not affect the ability of other sensory axons from terminating normally in the CZ protoglomerulus. In contrast  two members of the delta2 protocadherin family  pcdh10b and pcdh17  are most highly expressed in sensory neurons that project to the CZ protoglomerulus. Knocking down pcdh10b induces ectopic terminations of CZ projecting sensory axons. Knocking down pcdh17 induces substantial ectopic axonal trajectories and impairs CZ projecting sensory axons from finding and terminating in the CZ protoglomerulus. Knockdowns of either pcdh10b or pcdh17 do not affect DZ projecting sensory axons. These findings suggest that delta1 protocadherins help DZ projecting sensory axons enter and remain within the DZ protoglomerulus  while delta2 protocadherins help CZ projecting sensory axons navigate to the CZ protoglomerulus. Overall design: Roughly 2000 zebrafish embryos we sacraficed at 36  48 hpf and 72 hpf. Olfactory tissue was dissociated in FACSmax dissosciation medium and then FACsorted to isolate OMP:RFP positive neurons.,,,,OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish,GSM8838716,,source name:Olfactory Sensory Tissue|tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP|geo loc name:missing|collection date:missing,OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish,Cell Ranger V3.0.1 Assembly: GRCz11 Supplementary files format and content: Demultiplexed 10x Genomics Files.,Olfactory Sensory Tissue,,10X Genomics V3.3,,tissue:Olfactory Sensory Tissue|cell line:Olactory Sensory Neurons|cell type:Neurons|sample age:36 hpf|genotype:Tgomp:lyn RFP,GSM8838716,GSM8838716: OMP positive Olfactory Sensory Neurons from 36hpf Zebrafish; Danio rerio; RNA Seq,GSM8838716 r1,GSM8838716,1,10X Genomics V3.3,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP569567,,loader:fastq load.py,97366_S7_L002_I1_001.fastq.gz 97366_S7_L002_R1_001.fastq.gz 97366_S7_L002_R2_001.fastq.gz,fastq fastq fastq,5980615420.0,46004734.0,GSM8838716 r2,0:8 1:28 2:94,A:1289600464;C:857667521;G:934976316;T:1242064603;N:136092,8,28,94,,1289600464,857667521,934976316,1242064603,136092,SRX27953869,SRS24319773,SRA2091725,"Department of Neuroscience, University of Pennsylvania","Department of Neuroscience, University of Pennsylvania",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-03-11,Pharyngula,Embryo,Brain,Nervous System
35618,SRR32928249,SRX28203068,SRS24552774,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.H05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 8,78,78,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.H05.fq.gz,fastq,9110220.0,108455.0,expt2.broad.24.enzymatic.P01.H05.fq.gz,0:84,A:3384792;C:1565195;G:1973031;T:2182427;N:4775,84,,,,3384792,1565195,1973031,2182427,4775,SRX28203068,SRS24552774,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35619,SRR32928250,SRX28203067,SRS24552773,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.G05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 7,77,77,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.G05.fq.gz,fastq,4093068.0,48727.0,expt2.broad.24.enzymatic.P01.G05.fq.gz,0:84,A:1283703;C:801390;G:874961;T:1130908;N:2106,84,,,,1283703,801390,874961,1130908,2106,SRX28203067,SRS24552773,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35620,SRR32928251,SRX28203066,SRS24552772,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.F05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 6,76,76,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.F05.fq.gz,fastq,15414840.0,183510.0,expt2.broad.24.enzymatic.P01.F05.fq.gz,0:84,A:6868692;C:2274988;G:2950304;T:3312556;N:8300,84,,,,6868692,2274988,2950304,3312556,8300,SRX28203066,SRS24552772,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35621,SRR32928252,SRX28203065,SRS24552771,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.E05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 5,75,75,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.E05.fq.gz,fastq,7552440.0,89910.0,expt2.broad.24.enzymatic.P01.E05.fq.gz,0:84,A:2833004;C:1314546;G:1543833;T:1856906;N:4151,84,,,,2833004,1314546,1543833,1856906,4151,SRX28203065,SRS24552771,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35622,SRR32928253,SRX28203064,SRS24552770,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.D05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 4,74,74,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.D05.fq.gz,fastq,18449592.0,219638.0,expt2.broad.24.enzymatic.P01.D05.fq.gz,0:84,A:8110605;C:2781954;G:3613141;T:3933803;N:10089,84,,,,8110605,2781954,3613141,3933803,10089,SRX28203064,SRS24552770,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35623,SRR32928254,SRX28203063,SRS24552769,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.C05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 3,73,73,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.C05.fq.gz,fastq,5944344.0,70766.0,expt2.broad.24.enzymatic.P01.C05.fq.gz,0:84,A:2038886;C:1067891;G:1274553;T:1559956;N:3058,84,,,,2038886,1067891,1274553,1559956,3058,SRX28203063,SRS24552769,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35624,SRR32928255,SRX28203062,SRS24552768,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.B05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 2,72,72,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.B05.fq.gz,fastq,8608320.0,102480.0,expt2.broad.24.enzymatic.P01.B05.fq.gz,0:84,A:3054837;C:1594241;G:1754868;T:2199803;N:4571,84,,,,3054837,1594241,1754868,2199803,4571,SRX28203062,SRS24552768,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35625,SRR32928256,SRX28203061,SRS24552767,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.enzymatic.P01.A05.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  enzymatic dissociation  replicate 1,71,71,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.enzymatic.P01.A05.fq.gz,fastq,3979164.0,47371.0,expt2.broad.24.enzymatic.P01.A05.fq.gz,0:84,A:1268971;C:764759;G:844472;T:1098812;N:2150,84,,,,1268971,764759,844472,1098812,2150,SRX28203061,SRS24552767,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35679,SRR32928309,SRX28203007,SRS24552713,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.D05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 4,145,145,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.D05.fq.gz,fastq,364669704.0,4341306.0,expt2.deep.24.enzymatic.P01.D05.fq.gz,0:84,A:165363989;C:53167919;G:71115587;T:74956203;N:66006,84,,,,165363989,53167919,71115587,74956203,66006,SRX28203007,SRS24552713,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35680,SRR32928311,SRX28203006,SRS24552711,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.C05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 3,144,144,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.C05.fq.gz,fastq,79366728.0,944842.0,expt2.deep.24.enzymatic.P01.C05.fq.gz,0:84,A:30604656;C:12612645;G:16345725;T:19789600;N:14102,84,,,,30604656,12612645,16345725,19789600,14102,SRX28203006,SRS24552711,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35681,SRR32928312,SRX28203005,SRS24552712,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.B05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 2,143,143,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.B05.fq.gz,fastq,124887084.0,1486751.0,expt2.deep.24.enzymatic.P01.B05.fq.gz,0:84,A:49284416;C:21398883;G:23939821;T:30241510;N:22454,84,,,,49284416,21398883,23939821,30241510,22454,SRX28203005,SRS24552712,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35682,SRR32928313,SRX28203004,SRS24552710,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.A05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 1,142,142,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.A05.fq.gz,fastq,48850200.0,581550.0,expt2.deep.24.enzymatic.P01.A05.fq.gz,0:84,A:17085857;C:8742596;G:9989085;T:13024179;N:8483,84,,,,17085857,8742596,9989085,13024179,8483,SRX28203004,SRS24552710,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35683,SRR32928314,SRX28203003,SRS24552709,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.H08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 15,141,141,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.H08.fq.gz,fastq,105747516.0,1258899.0,expt2.deep.24.bead.P18.H08.fq.gz,0:84,A:39780997;C:18282450;G:21178201;T:26487273;N:18595,84,,,,39780997,18282450,21178201,26487273,18595,SRX28203003,SRS24552709,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35685,SRR32928316,SRX28203001,SRS24552707,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.H07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 14,140,140,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.H07.fq.gz,fastq,117293568.0,1396352.0,expt2.deep.24.bead.P18.H07.fq.gz,0:84,A:44388972;C:20447464;G:23549662;T:28886998;N:20472,84,,,,44388972,20447464,23549662,28886998,20472,SRX28203001,SRS24552707,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35686,SRR32928317,SRX28203000,SRS24552706,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.G08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 13,139,139,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.G08.fq.gz,fastq,141454152.0,1683978.0,expt2.deep.24.bead.P18.G08.fq.gz,0:84,A:51351272;C:25274905;G:28542033;T:36261200;N:24742,84,,,,51351272,25274905,28542033,36261200,24742,SRX28203000,SRS24552706,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35687,SRR32928318,SRX28202999,SRS24552704,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.G07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 12,138,138,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.G07.fq.gz,fastq,122244864.0,1455296.0,expt2.deep.24.bead.P18.G07.fq.gz,0:84,A:45925081;C:20992270;G:24808169;T:30497807;N:21537,84,,,,45925081,20992270,24808169,30497807,21537,SRX28202999,SRS24552704,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35688,SRR32928319,SRX28202998,SRS24552705,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.F08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 11,137,137,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.F08.fq.gz,fastq,128994264.0,1535646.0,expt2.deep.24.bead.P18.F08.fq.gz,0:84,A:48283607;C:21968133;G:25901679;T:32817928;N:22917,84,,,,48283607,21968133,25901679,32817928,22917,SRX28202998,SRS24552705,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35689,SRR32928320,SRX28202997,SRS24552703,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.F07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 10,136,136,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.F07.fq.gz,fastq,118856724.0,1414961.0,expt2.deep.24.bead.P18.F07.fq.gz,0:84,A:43763583;C:20413885;G:24105737;T:30552660;N:20859,84,,,,43763583,20413885,24105737,30552660,20859,SRX28202997,SRS24552703,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35690,SRR32928321,SRX28202996,SRS24552702,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.E08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 9,135,135,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.E08.fq.gz,fastq,93617076.0,1114489.0,expt2.deep.24.bead.P18.E08.fq.gz,0:84,A:34570395;C:16556476;G:18475268;T:23998365;N:16572,84,,,,34570395,16556476,18475268,23998365,16572,SRX28202996,SRS24552702,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35691,SRR32928322,SRX28202995,SRS24552701,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.E07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 8,134,134,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.E07.fq.gz,fastq,133722792.0,1591938.0,expt2.deep.24.bead.P18.E07.fq.gz,0:84,A:50066403;C:23328616;G:26650458;T:33653419;N:23896,84,,,,50066403,23328616,26650458,33653419,23896,SRX28202995,SRS24552701,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35692,SRR32928323,SRX28202994,SRS24552699,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.D08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 7,133,133,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.D08.fq.gz,fastq,106928304.0,1272956.0,expt2.deep.24.bead.P18.D08.fq.gz,0:84,A:40254325;C:17917465;G:21658773;T:27078732;N:19009,84,,,,40254325,17917465,21658773,27078732,19009,SRX28202994,SRS24552699,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35693,SRR32928324,SRX28202993,SRS24552700,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.D07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 6,132,132,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.D07.fq.gz,fastq,178733856.0,2127784.0,expt2.deep.24.bead.P18.D07.fq.gz,0:84,A:71103187;C:30043845;G:34285236;T:43269649;N:31939,84,,,,71103187,30043845,34285236,43269649,31939,SRX28202993,SRS24552700,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35694,SRR32928325,SRX28202992,SRS24552698,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.C08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 5,131,131,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.C08.fq.gz,fastq,118834296.0,1414694.0,expt2.deep.24.bead.P18.C08.fq.gz,0:84,A:43351162;C:20642531;G:24057336;T:30762255;N:21012,84,,,,43351162,20642531,24057336,30762255,21012,SRX28202992,SRS24552698,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35696,SRR32928327,SRX28202990,SRS24552696,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.C07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 4,130,130,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.C07.fq.gz,fastq,83413848.0,993022.0,expt2.deep.24.bead.P18.C07.fq.gz,0:84,A:31147177;C:14298386;G:16802760;T:21150889;N:14636,84,,,,31147177,14298386,16802760,21150889,14636,SRX28202990,SRS24552696,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35697,SRR32928328,SRX28202989,SRS24552695,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.B08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 3,129,129,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.B08.fq.gz,fastq,110508132.0,1315573.0,expt2.deep.24.bead.P18.B08.fq.gz,0:84,A:41593318;C:19375759;G:21744173;T:27775466;N:19416,84,,,,41593318,19375759,21744173,27775466,19416,SRX28202989,SRS24552695,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35698,SRR32928329,SRX28202988,SRS24552694,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.B07.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 2,128,128,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.B07.fq.gz,fastq,102579624.0,1221186.0,expt2.deep.24.bead.P18.B07.fq.gz,0:84,A:40321999;C:17087460;G:21685849;T:23466093;N:18223,84,,,,40321999,17087460,21685849,23466093,18223,SRX28202988,SRS24552694,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35699,SRR32928330,SRX28202987,SRS24552692,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.bead.P18.A08.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  bead dissociation  replicate 1,127,127,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.bead.P18.A08.fq.gz,fastq,108953208.0,1297062.0,expt2.deep.24.bead.P18.A08.fq.gz,0:84,A:40914540;C:18897489;G:22112695;T:27009444;N:19040,84,,,,40914540,18897489,22112695,27009444,19040,SRX28202987,SRS24552692,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35703,SRR32928334,SRX28202983,SRS24552689,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.H08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 15,70,70,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.H08.fq.gz,fastq,8144136.0,96954.0,expt2.broad.24.bead.P18.H08.fq.gz,0:84,A:2749870;C:1520663;G:1719585;T:2149644;N:4374,84,,,,2749870,1520663,1719585,2149644,4374,SRX28202983,SRS24552689,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35704,SRR32928335,SRX28202982,SRS24552687,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.H07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 14,69,69,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.H07.fq.gz,fastq,8916852.0,106153.0,expt2.broad.24.bead.P18.H07.fq.gz,0:84,A:3045003;C:1665942;G:1865766;T:2335320;N:4821,84,,,,3045003,1665942,1865766,2335320,4821,SRX28202982,SRS24552687,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35705,SRR32928336,SRX28202981,SRS24552688,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.G08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:13|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 13,68,68,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.G08.fq.gz,fastq,11133024.0,132536.0,expt2.broad.24.bead.P18.G08.fq.gz,0:84,A:3648380;C:2130637;G:2362380;T:2985637;N:5990,84,,,,3648380,2130637,2362380,2985637,5990,SRX28202981,SRS24552688,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35706,SRR32928337,SRX28202980,SRS24552686,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.G07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:12|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 12,67,67,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.G07.fq.gz,fastq,9315600.0,110900.0,expt2.broad.24.bead.P18.G07.fq.gz,0:84,A:3156213;C:1738465;G:1978549;T:2437568;N:4805,84,,,,3156213,1738465,1978549,2437568,4805,SRX28202980,SRS24552686,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35707,SRR32928338,SRX28202979,SRS24552685,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.F08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:11|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 11,66,66,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.F08.fq.gz,fastq,9789276.0,116539.0,expt2.broad.24.bead.P18.F08.fq.gz,0:84,A:3320270;C:1800281;G:2046649;T:2616905;N:5171,84,,,,3320270,1800281,2046649,2616905,5171,SRX28202979,SRS24552685,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35708,SRR32928339,SRX28202978,SRS24552684,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.F07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:10|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 10,65,65,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.F07.fq.gz,fastq,9214632.0,109698.0,expt2.broad.24.bead.P18.F07.fq.gz,0:84,A:3057793;C:1718213;G:1953657;T:2480102;N:4867,84,,,,3057793,1718213,1953657,2480102,4867,SRX28202978,SRS24552684,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35709,SRR32928340,SRX28202977,SRS24552682,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.E08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:9|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 9,64,64,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.E08.fq.gz,fastq,7261128.0,86442.0,expt2.broad.24.bead.P18.E08.fq.gz,0:84,A:2416194;C:1376949;G:1512433;T:1951817;N:3735,84,,,,2416194,1376949,1512433,1951817,3735,SRX28202977,SRS24552682,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35710,SRR32928341,SRX28202976,SRS24552683,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.E07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 8,63,63,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.E07.fq.gz,fastq,10062696.0,119794.0,expt2.broad.24.bead.P18.E07.fq.gz,0:84,A:3401117;C:1892628;G:2108920;T:2654785;N:5246,84,,,,3401117,1892628,2108920,2654785,5246,SRX28202976,SRS24552683,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35711,SRR32928342,SRX28202975,SRS24552681,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.D08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 7,62,62,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.D08.fq.gz,fastq,8198064.0,97596.0,expt2.broad.24.bead.P18.D08.fq.gz,0:84,A:2780756;C:1495133;G:1726582;T:2191139;N:4454,84,,,,2780756,1495133,1726582,2191139,4454,SRX28202975,SRS24552681,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35712,SRR32928343,SRX28202974,SRS24552680,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.D07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 6,61,61,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.D07.fq.gz,fastq,12509616.0,148924.0,expt2.broad.24.bead.P18.D07.fq.gz,0:84,A:4522316;C:2258311;G:2528248;T:3194042;N:6699,84,,,,4522316,2258311,2528248,3194042,6699,SRX28202974,SRS24552680,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35714,SRR32928345,SRX28202972,SRS24552677,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.C08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 5,60,60,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.C08.fq.gz,fastq,9391032.0,111798.0,expt2.broad.24.bead.P18.C08.fq.gz,0:84,A:3084926;C:1769610;G:1994555;T:2536912;N:5029,84,,,,3084926,1769610,1994555,2536912,5029,SRX28202972,SRS24552677,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35715,SRR32928346,SRX28202971,SRS24552678,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.C07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 4,59,59,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.C07.fq.gz,fastq,6317808.0,75212.0,expt2.broad.24.bead.P18.C07.fq.gz,0:84,A:2140905;C:1158658;G:1317321;T:1697538;N:3386,84,,,,2140905,1158658,1317321,1697538,3386,SRX28202971,SRS24552678,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35716,SRR32928347,SRX28202970,SRS24552676,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.B08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 3,58,58,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.B08.fq.gz,fastq,8412264.0,100146.0,expt2.broad.24.bead.P18.B08.fq.gz,0:84,A:2859217;C:1571503;G:1739845;T:2237036;N:4663,84,,,,2859217,1571503,1739845,2237036,4663,SRX28202970,SRS24552676,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35717,SRR32928348,SRX28202969,SRS24552675,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.B07.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 2,57,57,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.B07.fq.gz,fastq,7301532.0,86923.0,expt2.broad.24.bead.P18.B07.fq.gz,0:84,A:2597215;C:1318665;G:1571260;T:1810507;N:3885,84,,,,2597215,1318665,1571260,1810507,3885,SRX28202969,SRS24552675,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35718,SRR32928349,SRX28202968,SRS24552674,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.,,expt2.broad.24.bead.P18.A08.fq.gz,,seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  24hpf  bead dissociation  replicate 1,56,56,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.broad.24.bead.P18.A08.fq.gz,fastq,8205204.0,97681.0,expt2.broad.24.bead.P18.A08.fq.gz,0:84,A:2779647;C:1533064;G:1734713;T:2153264;N:4516,84,,,,2779647,1533064,1734713,2153264,4516,SRX28202968,SRS24552674,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35748,SRR32928380,SRX28202938,SRS24552644,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.H05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 8,149,149,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.H05.fq.gz,fastq,145976544.0,1737816.0,expt2.deep.24.enzymatic.P01.H05.fq.gz,0:84,A:60441236;C:22508438;G:31356971;T:31643952;N:25947,84,,,,60441236,22508438,31356971,31643952,25947,SRX28202938,SRS24552644,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35749,SRR32928381,SRX28202937,SRS24552643,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.G05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 7,148,148,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.G05.fq.gz,fastq,47683356.0,567659.0,expt2.deep.24.enzymatic.P01.G05.fq.gz,0:84,A:16326128;C:8784428;G:9655524;T:12908835;N:8441,84,,,,16326128,8784428,9655524,12908835,8441,SRX28202937,SRS24552643,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35750,SRR32928382,SRX28202936,SRS24552642,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.F05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 6,147,147,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.F05.fq.gz,fastq,277176648.0,3299722.0,expt2.deep.24.enzymatic.P01.F05.fq.gz,0:84,A:130211241;C:38031050;G:52145937;T:56738200;N:50220,84,,,,130211241,38031050,52145937,56738200,50220,SRX28202936,SRS24552642,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
35751,SRR32928383,SRX28202935,SRS24552641,SRP575522,PRJNA1244443,An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing,PRJNA1244443,Other,Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.,,,Sci plexRNAseq of a 24hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a relatively smaller number of cells in order to determine the number of UMIs produced by the method.,,expt2.deep.24.enzymatic.P01.E05.fq.gz,,seq depth:deep many umis|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:24 hpf|dev stage:24 hpf|collection date:2024 01 30|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal,,,,,,,,,sciPlex RNAseq of whole Danio rerio embryos: expt2  deep sequencing of limited cells  24hpf  enzymatic dissociation  replicate 5,146,146,Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.,,,OTHER,TRANSCRIPTOMIC SINGLE CELL,other,SINGLE,ILLUMINA,NextSeq 2000,,SRP575522,,,expt2.deep.24.enzymatic.P01.E05.fq.gz,fastq,118783980.0,1414095.0,expt2.deep.24.enzymatic.P01.E05.fq.gz,0:84,A:48417705;C:19064392;G:23595546;T:27685220;N:21117,84,,,,48417705,19064392,23595546,27685220,21117,SRX28202935,SRS24552641,SRA2104467,University of Washington|Genome Sciences,University of Washington,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq_v2,unknown,other,unknown,sc,single_cell_generic,generic-scrnaseq-only,,United States,2025-03-31,Pharyngula,Embryo,Whole Organism,All anatomical structures
66749,SRR23717086,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L001_R1_001.fastq.gz 210954C_spi2_MO_S1_L001_R2_001.fastq.gz,fastq fastq,38657555700.0,128858519.0,GSM7083029 r1,0:150 1:150,A:16254027461;C:6972577611;G:6733828903;T:8696771854;N:349871,150,150,,,16254027461,6972577611,6733828903,8696771854,349871,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92157,0.0,0.12849,1.0,0.7811,,0.5613,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66750,SRR23717087,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L002_R1_001.fastq.gz 210954C_spi2_MO_S1_L002_R2_001.fastq.gz,fastq fastq,39767723700.0,132559079.0,GSM7083029 r2,0:150 1:150,A:16740739613;C:7166687108;G:6926997738;T:8932937589;N:361652,150,150,,,16740739613,7166687108,6926997738,8932937589,361652,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92006,0.0,0.12624,1.0,0.7808,,0.56645,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66751,SRR23717088,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L003_R1_001.fastq.gz 210954C_spi2_MO_S1_L003_R2_001.fastq.gz,fastq fastq,33826342500.0,112754475.0,GSM7083029 r3,0:150 1:150,A:14247560719;C:6101219095;G:5882384356;T:7594866748;N:311582,150,150,,,14247560719,6101219095,5882384356,7594866748,311582,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91535,0.0,0.12519,1.0,0.7833,,0.56425,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66752,SRR23717089,SRX19578256,SRS16961238,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq spi2 morphant,GSM7083029,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq spi2 morphant,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM7083029,GSM7083029: 36 hpf Zebrafish VDA scRNA seq spi2 morphant; Danio rerio; RNA Seq,GSM7083029 r1,GSM7083029,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,210954C_spi2_MO_S1_L004_R1_001.fastq.gz 210954C_spi2_MO_S1_L004_R2_001.fastq.gz,fastq fastq,42436674900.0,141455583.0,GSM7083029 r4,0:150 1:150,A:17850346993;C:7641162936;G:7380219938;T:9564565232;N:379801,150,150,,,17850346993,7641162936,7380219938,9564565232,379801,SRX19578256,SRS16961238,SRA1601408,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.91972,0.0,0.12638,1.0,0.78131,,0.56385,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2023-03-06,Pharyngula,Embryo,Multi-tissue,Multi-system
66753,SRR16539848,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_1_1_R1.fq.gz 190718O_ECHEHSC_R_1_1_R2.fq.gz,fastq fastq,42862683000.0,142875610.0,GSM5651458 r1,0:150 1:150,A:19056076938;C:7513613524;G:7148399243;T:9144249423;N:343872,150,150,,,19056076938,7513613524,7148399243,9144249423,343872,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92848,0.0,0.09872,1.0,0.81797,,0.52595,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66754,SRR16539849,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_2_1_R1.fq.gz 190718O_ECHEHSC_R_2_1_R2.fq.gz,fastq fastq,45613780500.0,152045935.0,GSM5651458 r2,0:150 1:150,A:20279847027;C:7989810705;G:7602659881;T:9741099780;N:363107,150,150,,,20279847027,7989810705,7602659881,9741099780,363107,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92821,0.0,0.09747,1.0,0.81706,,0.52451,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66755,SRR16539850,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_3_1_R1.fq.gz 190718O_ECHEHSC_R_3_1_R2.fq.gz,fastq fastq,57137293500.0,190457645.0,GSM5651458 r3,0:150 1:150,A:25401821096;C:10031650741;G:9533037288;T:12170324099;N:460276,150,150,,,25401821096,10031650741,9533037288,12170324099,460276,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92958,0.0,0.09774,1.0,0.81773,,0.52455,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
66756,SRR16539851,SRX12742420,SRS10690646,SRP342742,PRJNA773777,Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity [Zebrafish.scRNA seq],GSE186423,Transcriptome Analysis,Using a combination of single cell multi omics  lineage tracing and functional assays  we show that embryonic HSPCs are originated from heterogeneous hemogenic endothelial cells HECs during zebrafish embryogenesis. Overall design: Hematopoietic stem and progenitor cells HSPCs are considered as a heterogeneous population  but where and how HSPC heterogeneity occurs remain unclear. Here  we performed scRNA seq and scATAC seq with zebrafish 36 hpf VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells. To determine the transcriptional signatures of spi2+ lineages in zebrafish  we performed STRT seq with spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells at 36 hpf. To investigate the underlying molecular mechanism upon spi2 deficiency  we performed scRNA seq with the sorted ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ from spi2 morphants at 36 hpf. To determine whether spi2 can directly modulate transcriptional programs in EC/HEC  we examined genome wide spi2 binding by cut tag assay in fli1a flag spi2 EGFP+ cells sorted from trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf.,parent bioproject:PRJNA773771,pubmed:37016019,,36 hpf Zebrafish VDA scRNA seq,GSM5651458,,source name:Zebrafish VDA|tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,36 hpf Zebrafish VDA scRNA seq,For scRNA seq  and scATAC seq based on 10x Genomics，raw data files were processed by Cell Ranger software suite with default mapping parameters  using the GRCz11 reference genome. For STRT seq  raw reads were first de multiplexed by barcode sequences in reads 2 to yield separate read files for individual cells  then the transcripts sequences of each cell in reads 1 were separated based on corresponding reads 2. Simultaneously  UMI sequences in reads 2 were integrated into reads 1. The template switching oligo TSO sequence  polyA sequence and the low quality reads N > 10% in reads 1 were subsequently removed by Python scripts and Trimmomatic version 0.36. Next  the clean reads were aligned to the zebrafish genome GRCz11 from Ensembl using HISAT2 version 2.1.0 with known gene annotation. Only protein coding genes were retained and the abundance of each gene were estimated by counting the reads that duplicated UMIs have been excluded. For cut&tag  reads were aligned to GRCz11 by Bowtie2. Only uniquely mapped reads with mapping quality score ≥ 30 were kept using Samtools software. post merging replicates  MACS2 was used for the peak calling. Assembly: GRCz11,Zebrafish VDA,,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell 3’ Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,tissue:Zebrafish VDA 36hpf|cells:VDA derived kdrl+runx1   kdrl+runx1+  and kdrl runx1+ cells|Stage:36 hpf,GSM5651458,GSM5651458: 36 hpf Zebrafish VDA scRNA seq; Danio rerio; RNA Seq,GSM5651458 r1,GSM5651458,1,For 10x Genomics based scRNA seq and scATAC seq in zebrafish  40 000 mCherry+ GFP  cells  40 000 mCherry+ GFP+ cells and 30 000 mCherry  GFP+ cells were sorted from Tg kdrl:mCherry/runx1:enGFP at 36 hpf. For STRT seq in zebrafish  single spi2: Gal4;UAS:GFP+ kdrl:mCherry+ HECs and spi2: Gal4;UAS:GFP+ kdrl:mCherry  hematopoietic cells were sorted from the trunk region of Tg spi2: Gal4;UAS:GFP/ kdrl:mCherry at 36 hpf. For scRNA seq of spi2 morphants at 36 hpf in zebrafish  ECs kdrl+runx1   HECs kdrl+runx1+ and hematopoietic cells kdrl runx1+ were sorted. For bulk CUT&TAG in zebrafish  fli1a flag spi2 EGFP+ cells were sorted from the trunk region of Tg fli1a flag spi2 GFP embryos at 36 hpf. For 10x Genomics based scRNA seq and scATAC seq in zebrafish  we loaded 20 000 cells for further 10x Genomics based scRNA seq and 90 000 cells for further 10x Genomics based scATAC seq. For scRNA seq  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For ATAC seq  nuclei were isolated and washed according to the methods supplied by 10x Genomics. Libraries were prepared using the Chromium Chip E Single Cell Kit and Chromium Single Cell ATAC Library & Gel Bead Kit  and further sequenced on an Illumina Novaseq6000 platform to generate 50 bp paired end reads. For 10x Genomics based scRNA seq in mice  libraries were prepared using Single Cell three prime Library and Gel Bead Kit V3.1. Sequencing was performed on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For STRT seq in zebrafish  the end repair and dA tailing of the DNA fragments and ligation of the adaptors to the DNA fragments were performed according to the KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series. post the adaptor ligation step  the final PCR was performed. The libraries were sequenced on an Illumina Novaseq6000 platform to generate 150 bp paired end reads. For bulk CUT&TAG  libraries were prepared according to Hyperactive In Situ ChIP Library Prep Kit for Illumina and sequenced on an Illumina NovaSeq6000 platform to generate 150 bp paired end reads.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP342742,,,190718O_ECHEHSC_R_4_1_R1.fq.gz 190718O_ECHEHSC_R_4_1_R2.fq.gz,fastq fastq,29835023100.0,99450077.0,GSM5651458 r4,0:150 1:150,A:13290644326;C:5233486555;G:4966979633;T:6343677510;N:235076,150,150,,,13290644326,5233486555,4966979633,6343677510,235076,SRX12742420,SRS10690646,SRA1600571,"Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES","Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES",2,0.0,0.92872,0.0,0.098,1.0,0.8185,,0.52198,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2021-10-22,Pharyngula,Embryo,Multi-tissue,Multi-system
69677,SRR19094454,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L001.fastq.gz,fastq,68847033000.0,688470330.0,GSM6107905 r1,0:100,A:23357162980;C:13669902202;G:15661490477;T:16154844400;N:3632941,100,,,,23357162980,13669902202,15661490477,16154844400,3632941,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.7254,,0.3995,,0.84149,,0.56669,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
69678,SRR19094455,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L002.fastq.gz,fastq,64445114000.0,644451140.0,GSM6107905 r2,0:100,A:21755385809;C:12837761861;G:14651336119;T:15197372623;N:3257588,100,,,,21755385809,12837761861,14651336119,15197372623,3257588,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.73455,,0.40204,,0.84153,,0.56626,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures
69679,SRR19094456,SRX15162537,SRS12904064,SRP373785,PRJNA835404,Proteostasis governs differential temperature sensitivity across embryonic cell types,GSE202294,Other,The genetic program of embryonic development is remarkably robust  but temperature stress can degrade its ability to generate animals with invariant anatomy. While the stereotyped  consistent phenotypes associated with environmental stress during vertebrate development suggest that some cell types are more sensitive to stress than others  the basis of this sensitivity is unknown. Here  we characterize hundreds of individual zebrafish embryos under temperature stress using whole animal single cell RNA seq to identify cell types and molecular programs within them that drive phenotypic variability. We find that temperature perturbs the normal proportions and gene expression programs of numerous cell types and also introduces asynchrony in their development. The notochord is particularly sensitive to temperature stress  which we show is due to a specialized cell type  sheath cells. Further analyses show that sheath cells accumulate misfolded protein at elevated temperature  leading to a cascading structural failure of the notochord and irreversible anatomic defects in the embryo. Our study demonstrates that whole animal single cell RNA seq can characterize mechanisms important for developmental robustness and pinpoint molecular programs within specific cell types that constitute key failure points. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to temperature perturbations 28C  32C  34C with sci RNA seq3.,,pubmed:37949057,,Hotfish,GSM6107905,,source name:Whole embryo|tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,Hotfish,The demultiplexing  barcoded processing  gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: hotfish.cds monocle3 object Supplementary files format and content: HF4 counts.RDS gene by cell counts  sparse matrix Supplementary files format and content: HF4 cell metadata.txt cell metadata  tab separated Supplementary files format and content: HF4 gene metadata.txt gene metadata  tab separated Supplementary files format and content: HF4 hash sampleSheet.txt hash sample table  tab separated Supplementary files format and content: HF4 processed hashTable.csv hash count table  tab separated,Whole embryo,,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,Zebrafish embryos were raised in embryo media at 28.5  32  and 34C.,tissue:Whole embryo|developmental stage:24  30  36 hpf|strain:AB|genotype:wild type|treatment:temperature perturbation experiment controls  treated|temperature:28C  32C  34C|fraction:nuclear polyA RNA,GSM6107905,GSM6107905: Hotfish; Danio rerio; RNA Seq,GSM6107905 r1,GSM6107905,1,Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope  which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS  5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis  tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it  a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. snRNA seq,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP373785,,loader:fastq load.py|options:  appendBCtoName,HF4-L003.fastq.gz,fastq,67150909400.0,671509094.0,GSM6107905 r3,0:100,A:22732764240;C:13367603512;G:15251969605;T:15795309966;N:3262077,100,,,,22732764240,13367603512,15251969605,15795309966,3262077,SRX15162537,SRS12904064,SRA1415795,University of Washington,University of Washington,1,0.73136,,0.39771,,0.83796,,0.45674,,100,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_plate,scirnaseq,,United States,2022-05-05,Pharyngula,Embryo,Whole Organism,All anatomical structures